With research couldn't find anything reported similar. Tested the Query on AX 2012 R3 CU9, following the below repro steps but couldn't replicate the issue.
Steps:
1. Project III license is turned off.
2. Go to Project management and accounting/Common/Projects/All projects and create a new project with type ‘’Fixed price’’ and create a new project contract too on the same form
3. On the ‘In process’ project go to Action pane/Manage/Bill/On-account transactions
4. Create a new record in the On-account form and define a sales price
5. Go to the project contract created for the project
6. On the Action pane/Maintain/New select invoice proposal
7. Create and post the invoice proposal
8. Go back to the project and on the Action pane/Manage/Bill select the On-account transactions
9. On the on-account form select Functions/Select for credit note option
10. Select the one that you want to credit and hit OK
11. On click of ‘’ok’’, the form ‘’select for credit note’’ closes and on the on-account form, sales tab, the status is ‘’selected for credit note’’
12. On the project form, click on ‘’Invoice proposal’’ under ‘’New’’ in the action pane and a new create invoice proposal screen pops up with a negative value of - 200
13. Click ‘ok’ on the create invoice proposal form and post the invoice proposal.
14. the posting happens successfully.
these are my repro steps.
but customer not able to do successfully.