Yes, it is, @matt is right. The repository format is designed in such a way so that files in the repo are only ever added or removed completely, never changed. Besides lock files (in the locks/ dir), the only operations which remove files are prune and forget. When you do not run these operations while the sync to the cloud is still in progress, you’re fine. A run of backup for example will only add completely new files to the data/, index/ and snapshots/ directories.
You got everything right as far as I can see 