I have tried Apply Deposits and Apply Payments from the Bank Deposits Journal and the Bank Payments Journal and both work correctly in 2.22.3.
I have also tried Apply > Deposits and Apply > Payments in the bank account and both work perfectly.
I do recall that neither worked correctly in 2.15.X (?) but now in 2.22.3 both scripts are working correctly.
I used Apply Deposits with the following options:
3. warning and errors
5. No and Ye
I also used the above options with Apply Payments.
What version of NV2 are you using. Upgrade to the current version (2.22.3) and retry again. Review Help > About in your NV2 books to review your current NV2 version.
If you have any questions or concerns, you can email me at email@example.com
Regards to All,