We'll need more details to help us answer your question. You'll need to either get access to SL or better yet get help from the users that actually perform the processes to described exactly what they are doing and where.
MY guess right now is that your users may be using Flexible Billings in the Project module since that screen module has a specific "thing" called an Invoice reversal which does automatically generate an AR Credit memo which sound consistent with some of what you described.
Of course it's also possible that they are using Order Management or just booking things straight in AR.
No matter what, I at least will need a little more detail about what your users are doing and also some more specifics about exactly what you are trying to get to be able to assist.
Regards,
Tom Malia
T&T Data Solutions L.L.C.