VST Connect Pro 3 HD File Transfer Issues

Not quite sure what you mean by that.

Again I don’t know what you mean by that.
It makes no sense to transfer automatically after each recording, because you may want to skip that take anyways.
Once “Get HD Files” is initiated, it does work in the background. Alternatively, one can transfer the files by other method (DropBox etc) and use “Get Local HD Files”.
We do multiple recordings, drop in/out and even editing of Performer takes and Get HD Files works as expected. We would have to know how exactly you work. I guess you might run into problems when you get into heavy lane editing or the like, although even that should work as long as no new edits are produced (like applying process like pitch shift etc to such recordings), which you should do after Get HD.