Wow 100,000 employees and you're still using Access! It sounds from the symptoms you describe someone has been messing with your access tables and have removed/changed the linkage.
I worked in a 'Large' company that had just 2000 employees, we abandoned Access RDB tables long ago, we had the main employee database an Oracle HR system, this fed the Billing Matrix and all the other systems that used the unique employee number as primary key.
Because most of our data was held on Oracle systems, we used Business Objects software to produce extremely complex reports very quickly.
The only DB that wasn't linked was the training
system, this was a dogs dinner of a system built using Access db and front end, it was poor when built, but because the system used the employees surname rather than his/her unique employee number, as more data was added it has become worse and worse.
Several of our employees have the same name, some even have the same first, middle and surname, but because this database isn't linked people get mixed up, some who have to attend training courses by law every year have never attended them, others are put on unnecessary courses costing thousands!
Moral of the story is get one reliable master rDB to feed the other systems or risk corrupting your data.