I've used the following for cleaning up Custom Reports. The first couple steps may be applicable to you. Then maybe start at step 11 to recompile.
How to remove reports from Custom Report that have been deleted through Report Manager Resolution ID: 438688
Entry Type: Informational
Product: Sage MAS 90 ERP, Sage MAS 200 ERP
Application: Library Master
Version Reported: 4.0
Subject:
How to remove reports from Custom Reports that have already been deleted through Report Manager.
Possible Resolution:
Delete the records from Data File Display and Maintenance, and recompile the menus.
1.Open Library Master / Utilities / Data File Display and Maintenance.
2.In the 'Filename' field, enter ""SY_MENU"" (without quotes).
3.Browse to the record that references the report that needs to be removed, and click the 'Delete' button.
4.In the 'Filename' field, enter ""SY_TASK"" (without quotes).
5.Browse to the record that references the report that needs to be removed, and click the 'Delete' button.
6.In the 'Filename' field, enter ""SY1RPM"" (without quotes).
7.Browse to the record that references the report that needs to be removed, and click the 'Delete' button.
8.SY1RPP ALSO
9.In the 'Filename' field, enter ""SY1FRM"" (without quotes).
10.Browse to the record that references the report that needs to be removed, and click the 'Delete' button.
11.Recompile the menus.
a.From the Business Desktop, select File / Run.
b.Type ""SYZCON"" (without quotes) and click 'OK'.
c.At the --> prompt, enter the following and press ENTER after each line:
menus=new(""sy_menu_svc"",%sys_ss)
? menus'compilemenu()
drop object menus
bye
Note: The compile menu returns a 1 for success and a 0 for failure.