I'm curious about this statement. Could you give an example or two?
I believe the B7 A4 MED9 are troublesome with clone tools, but I've never had the need to try.
My tool has so far flashed:
2005 A3 2.0 TFSI
2006 Golf GTI
2008 8P S3
2010 Cupra R
2010 Golf R
2012 Golf R
2012 ED35
The only problems I've ever had during a read or write has been laptop battery related. The tool has ALWAYS recovered over the port without issue.