With regard to Office Ally:
If you do not keep track of some kind of identifier, it can be difficult to know whether a patient is in the O.A. database when they come in for a visit - particularly if they have not been in for a while. The default position, particularly in a busy office, is to simply create a new patient record. In doing so, you have instantly created a duplicate account. And, unfortunately, spelling mistakes and/or typing in "Dan" while the original record has "Daniel", makes it almost impossible to find the "correct" original record.
Over time, in an office staffed with folks for whom it is easier to create a duplicate record than to find the original record, you are going to end up with a database that is full of duplicate, triplicate, fourthlicate, etc. patient records.
Three points you did not mention are 1) how long has the provider been using Office Ally; 2) were duplicate records deleted before the old database was imported into Office Ally at the start, and; 3) how long ago was this new biller hired?
I don't know of any way to figure this out in your situation (don't know how your Office Ally is set up), but I will mention it just to trigger some thoughts if you have not thought about this: Office Ally only allows you to delete a record if there has been nothing placed into it regarding an office visit. If something has been placed there, including I think just an appointment being recorded, Office Ally will not let you delete the record. But it does give you a means of "hiding" the record. It is still in the database, but it is not pulled up into anything you can see on-screen. Office Ally also gives the user a means of unhiding records that have been hidden. This, then, makes the hidden record become visible.
Office Ally also provides a means of merging records. So, if I have 5 duplicate records, I can pick the record I want to keep (by account # or patient name) and Office Ally will merge the data in the other four records into that one record that I designated.
It is possible that the new biller knows all of these things about Office Ally and is simply cleaning up the database. Remember, Office Ally won't let anyone, including this new biller, delete a record that has something in it. So - the new biller is either hiding duplicate records (not the best solution unless someone is deceased), or they are merging duplicate records into one.
Hopefully this information will encourage you to approach what you think you see from a more-informed angle. Billers CAN do many illegal things. Office Ally makes it harder for that to happen.