Assuming the marks are still Change Markers and haven't been exploded in the other layout then you just need to select each one and relink it to the relevant revision. The corrupt marks were probably "Source" references, you now need the new duplicates to be "Linked"
Apple iMac macOS Monterey / AC26UKI (most recent builds)
You can go to Transmittal Set Details dialog box for the current Transmittal Set, the'Create New Revision in all Included Layouts' is always checked for a project's first Transmittal Set. This will assign a new revision ID for every layout you've added regardless if it doesn't contain any changes. Uncheck this setting and I hope it works.
ArchiCAD 18-26 | Twinmotion 2022 Mac Mini (M1, 2020) | macOS Monterey | Apple M1
HP Victus | Windows 11 | 16.0 GB RAM | AMD Ryzen 7 5800H with Radeon Graphics 3.20 GHz