Syncing between old and new format

Hello community.
I am having an issue when I turn on the OneDrive syncing for my vault folder. This folder has been synced to cloud before with the old vault format. A couple weeks ago, I stopped syncing it.

Recently, I update the newest version of Cryptomator. With this update, the program asks me to convert to new vault format. I accept and it converts successfully for the local data in my computer. After that, I decide to turn the syncing on again, hoping it will update changes to cloud. But for half of the day, I notice the OneDrive is downloading tons of things. I turn off syncing immediately because I doubt it downloading old vault files.

I then use another hard drive to save all the cloud folder (old format). Now, something’s very weird.

The data in new vault format (data in my computer), have some files duplicated. For example, there is a file named “abc.jpg”, but now there is “abc (1).jpg” also. Not all files are duplicated, just some (I guess 1/5 of the total)

The data in old vault format (data in my external drive), have been duplicated also. Again, not every file is duplicated, but about 4/5 of the total, I mean, a lot).

Checking randomly some files, they are still normal, no sign of corrupting.

My question is: Will there be a change that some files are corrupted (data in new format)?

To clear the duplicated file, I search with keyword (datecreated:yesterday, the keyword in Windows 10 that helps me find the files which are created yesterday. I use it because when comparing abc.jpg and abc (1).jpg, they have different created date). But I still fear of deleting some of my original files.
Any advice for that?

Thank you for reading my post. I guess it’s a bit complicated.!
example of duplicated files