Please do upgrade the project first.
1.Open Project Administrator enable Integrity Check in the Edit>Preferences dialog.
2. It should run automatically, but if not right click on the project and select revalidate.
3.once the integrity check completes, right-click on the project again and choose Upgrade>From Integrity Check Results.
4. Now, open the project in Administrator and it should upgrade project and add it to the new DB3 file. So, you must do this for each project.
If this is done, maybe check the APCUSTDIR path definition in PROJECT.INI. If it is blank, or shows red.. you may need to adjust it.