Going from an input to output between builds means that a drive conflict could occur at next launch. If that happens I have found out the hard way that the part will not load.
Sorry, it is unclear to us what you mean. Can you explain in more detail what your problem actually is?
Depending upon your actual issues potentially useful FAQs might be:
Regaining debug access to target MCU
ISP Reset over debug
You might also want to look at the "Debugger Disconnect" behaviour setting in the Launch Configuration:
Launch Configuration Menu
We now have an FAQ covering the "Debugger Disconnect" behviour
Retrieving data ...