Yes, I found that same post in the Box community after posting here.
I may have found a surprisingly simple fix. I got fed up with warnings and so started to copy my RStudio project folder out of my Box Drive. The folder is so big that I gave up after 10 minutes or so. But when I subsequently reopened the project on Box Drive, I did not get any warnings/messages.
So here is what I believe might be happening. Box Drive caches on demand. So you can potentially open a folder and it may take awhile for the entire contents to appear. If you write a file with the same name as a file that is being reloaded from the remote Box server, you will, I assume, get a conflict warning. By attempting to copy the folder out of Box Drive, I might have forced Box Drive to cache the entire folder contents locally.
It seems the real fix might be for Box to implement a method to force a folder to sync up before writing anything into the folder. This is a guess but consistent with the behavior I just described.
Thanks for looking into this.