FileMaker automatically saves all data entered into fields with regular storage. Global fields are the exception as changes to global fields made from a client computer will not be saved.
It's unlikely that the difference in versions is an issue unless there is a script involved that uses Features added to Filemaker after the release of 8.5.
You'll need to consider the following options:
Is there a delete option specified in a relationship that shouldn't be there such that these records are being deleted automatically when a related record is deleted? If the "batches" all have a common value used to link to a related record, take a close look at all your relationships.
Check your file for damage--both damage to the file's structure and damage to a field's index. A damaged index can keep a find or sort from working correctly and this can create the illusion that records are missing. You can run a recover on the file to see if any issues are reported. Since the recovered file will have all field indexes rebuilt, you can check the recovered copy even if no problems were found to see if your missing records are no longer missing.
Is there a script that was run shortly before the records went missing? Maybe a script has modified data or deleted records in a way that is shouldn't. Go to Related Records can be the culprit for this if you have a script that modifies/deletes data in related records after Go To Related Records is used to pull them up in a found set. If your script doesn't check to be sure that there are related records to go to, the script might proceed to execute the rest of the steps on a completely wrong layout and set of records.
Also, how to you open and modify data in this "co-worker's database"? If it is in a shared directory and you are opening it by double click or via File | Open instead of Open Remote..., then you may have damaged the database. If the file is in a drop box or other type "cloud server" account, the changes from one of you may have overwritten changes made by the other if you both had the file open at the same time.
...and finally check that you aren't entering short batches of data actually in Find mode.