For files that exist on both sides, the default during --resync is that the version from Path1 will overwrite the version from Path2. So in your case, ~/Cloud would overwrite protondrive:Cloud (but of course, you could change that by just switching the order of the args.)
In v1.66 (currently available in beta), there is a new --resync-mode feature which allows much greater control over this. It allows you to specify things like --resync-mode newer (the newer file wins), --resync-mode larger (the larger file wins), --resync-mode path2 (the version from Path2 wins), etc. See the docs for more details.
I'm not a ProtonDrive expert, but my read of --protondrive-enable-caching is that the warning is talking about the VFS (the caching system used for rclone mount and rclone serve.) bisync and sync do not use the VFS (unless you are syncing into a mount or something, which I wouldn't recommend), so I don't think the --protondrive-enable-caching warning applies in your case. But perhaps another ProtonDrive user here can chime in here to confirm whether my read of the docs is correct.
What I would say, however, is that it's generally not a great idea to run multiple sync / bisync jobs concurrently to overlapping paths (of any remote), as that is inherently prone to race conditions. See FAQ
I would additionally caution that ProtonDrive is in beta and uses an unofficial API. There have been several reports here that it is not entirely stable at the moment, so I probably wouldn't recommend using it for anything too mission-critical.