I posted about the changes to OneDrive recently, and share your assessment; there is an example of a user probably experiencing the effects linked from that thread.
I wasn’t aware until now that Dropbox was also changing its folder location, so thanks for that link; again, I agree this is likely to cause trouble. I see the potential for data loss when the change is implemented. Specifically, I see a problem if the location is changed on one Mac, but not (immediately) on the other. Whether or not that happens may or may not be something the user has influence over. As I explained here that mechanism certainly has the potential to cause data loss.
That thread is on the subject of sync rather than indexing; Criss explains in that thread that sync should not be affected.