You’re mixing two things here - sync and indexing. Indexing a cloud location is supported only if that location has a local mirror which contains the files in question. Until now, that was the behaviour shown by OneDrive. As I noted here that behaviour is changing; Microsoft have more details on those changes here.
Whilst other users have reported no problem with the change due to the original local OneDrive folder being replaced by a symlink to the new folder, indexing will still require that you make the local files permanent (see the Microsoft support document I referenced above on how to do that). Three things to do, then: first, before proceeding, please make sure you have a backup of the files in your OneDrive folder. Although to my knowledge there have been no reports here of data loss with regard these changes, based on my limited knowledge I still assume that there is a possibility for data loss in some cases; set the files to be permanently available locally; possibly change the pointer to the location of the files in DT from the previous location to the new location (again, the support document will provide more details). I would guess that those two changes might solve your problem.
The issue could have arisen - I guess - when you synced DT across two Macs which were using different OneDrive versions (and thus different file paths). Is that possible? Obviously then the solution would be to make sure all devices are using the same setup and software versions.