Your question leaves much unclear. I'll have a go at it anyway.
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first aspects
A chip which requires reprogramming can be any of several sorts, and programming each sort will differ. There are, for instance, various kinds of ROM. Factory programmed ROMs cannot be reprogrammed at all.
* PROM chips are a variety of field programmable ROMs, much like EPROMs, but cannot be erased as they aren't EEPROMs and lack the UV erasure window on the chip found in EPROMs.
* EPROM can be erased (with special purpose high intensity UV light in special erase devices -- ordinary light does not work) adn then reprogrammed using any of several special programmers (several suppliers and quite a range of quality and pricing too) which applies precise patterns of voltage and timing, Most such chips can be programmed and reprogrammed a small number of times (tens, perhaps; certainly not thousands)..
* EEPROM can be erased electrically, though often not in eht end use circuit, using special purpose equipment. It can then be reprogrammed, sometimes in the same programming equipment. Again there are several manufacturers and a range in price an quality. Most such chips can be programmed and reprogrammed a small number of times (tens, perhaps; certainly not thousands) just as with EPROMs..
* FLASH ROM, a variety of EEPROM which is often found in circuits supporting in-circuit erasure and reprogramming. This is the most commonly encountered type in USB thumb drives, some iPod type equipment, etc. For many years, the BIOS chips in most computers have been of this type. These chips are intended for repeated erase / reprogram cycles, generally many hundreds and perhaps thousands of times. However, the lifetime is of specific memory cells (one bit) and failures are neither uniform nor predictable. Thus, a paticular bit cell might fail, leaving all others still functional. If that bit is in an important data structure (inthe thumb drive directory, for instance), then large amounts of data can become unusable.
* Programmable circuits such as F(ield)P(rogrammable)L(ogic)A(rray) which can be programmed by the user in the field to have this electrical behavior rather than that. Some of these are reprogrammable, some are not, some are multi programmable, some only a few times... Programming and erasure require special patterns and timing of special voltages, rather like EPROMs or EEPROMs. Again, there are several vendors of programming / reprogramming equipment, with a considerable variation in price and quality.
* Hybrid circuits, such as microcontrollers with a small amount of ROM (any type in principle, EEPROM most usually, FLASH sometimes) on the chip. These are usually found embedded in other equipment in their intended use. For instance, the 'intelligence' in a microwave oven is a program, usually in ROM of some kind on the microprocessor chip in the oven. Or in the micro chip which makes possible the behavior of, say, Furby (of some years ago). When made in large numbers, it is economically sensible to avoid more expensive programmable ROMs and to use a factory burned ROM type.
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programming
Most programmers are capable of working with several types of chips. The flexibility they aspire to ("Thousands of devices supported!") is part of the reason they vary considerably in price, quality, and support. Support is important because new chips requiring more or less different programming voltages and timing patterns are continually being released. And existing chips revised with new production runs, or the discovery of improved algorithms for existing chips. The conversion of these semiconductor manufacturer specifications to instructions for particular progamming equipment (ie, voltage patterns and timings) is done by the programmer supplier, and end users (ie, those out at the burning end of things) are completely dependent on the quality and promptness of their work. A new chip which is not supported by a particular programmer for months (or ever) can be a considerable problem. Many shops which require chip programming usually have more than one programmer on hand from at least two different vendors. And are willing to pay substantially for programming hardware not much different than less expensive programmers, but with more consistent and reliable support.
Most of the flexibility is accomodated by controlling the programmer hardware from a PC type computer. Modern programmers usually connect over a parallel port, but older designs sometimes required a plugin bus card. The software for programming equiment, and the data to be programmed (eg, programs, or actual data, or circuit descriptions (for FPLAs and the like)) are stored on disk.
It is sensible to use a dedicated standalone computer for this, since one with a variety of tasks and processes running may not be able to meet the precise timings required for reliable programming of devices. And, the machine should have all unneeded tasks, services, daemons, background processes, etc turned off, for the same reasons.
Production programmers (called 'gang programmers') have all the same considerations, and limitations, of single chip programmers, but with the problem that misprogramming can be much more expensive. Eight ruined $25 programmable chips is rather more expensive than one, after all.
Programming a chip takes time and how long depends on 1) the size of the chip (a 2KB PROM can be burned rather faster than a !MB PROM), 2) the programming algorithm the chip requires (chips cannot be reliably programmed faster than this), and 3) the capabilities of the programmer and its software. Programming 540 chips can take very many, tedious, hours. Part of the tedium is due to the exquiste care required in handling them to prevent electrostatic damage, which can happen without warning and permanently ruin a chip's functionality. Modern chips are both larger and more easily damaged than older chips. Static protection measures are required for anyone programming standalone chips.
And, chips come in various packages. It's possible that the same chip die can be supplied in DIP, PGA, BGA, surface mount, etc. They must be programmed in exactly the same way electrically, but handling each package type is quite different. Adapters are available for most packages, which electrically convert the chip to a form suited to insertion into a programmer. They tend to be expensive, probably because demand is quite low.
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content and content preparation
All of the data in such chips is usually called firmware, especially if it is kept in a reprogrammable chip, except that the information burned into such chips as FPLAs is almost never referred to as firmware.
Depending on the purpose, and on the type of chip in which the information is meant to be burned, its preparation can require a considerable amount of work and special tools. FPLAs and similar chips require preparation with special purpose 'compiler' programs available from the chip manufacturers. Data meant for ordianry PROMs is prepared using whatever tools are usually used (asemblers, compilers, etc) and the resulting files burned into the PROMs. However, depending on the system design, speical formats fo rthat data may be required. For example, byte 1 (or even bit 1) may have to be in one PROM, while byte 2 (or bit 2) is placed in the next. This will require special tools to transofrm the file being burned as needed.
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testing
Since many PROMs are installed in customer equipment that may not be available to those doing the burning, quality testing for the burned PROM can be a problem. Most programmers have a 'read and test against the file being burned' function, and it should be used. But it's insufficient both in principle and practice as a correctly programmed part containing the wrong data or code can't be identified without actual operating tests.
Perhaps some of this has illuminated your problem?