This is more of an informative post, that will help you take a look at the logs generated when communicating with AVR tools and devices, when something bad in debugging happens and want to send logs back to atmel or take a look by yourself. Though I am not the expert in how to debug the debugging related stuff in Studio, I would address myself as more of a Studio evangelist in this case, and spread the tricks around.
To generate logs for backend, goto your local application data\Atmel and delete the folder codeCache
Goto Installation directory and inside that goto avrdbg folder. copy the following contents and create a file by name avrdbg.properties and put that file inside that folder.
# Atmel configuration
logging.loggers.root.channel = c2
logging.loggers.root.level = trace
logging.formatters.f1.class = PatternFormatter
logging.formatters.f1.pattern = %h %M %S %i: %s %t
logging.channels.c2.class = FileChannel
logging.channels.c2.path = c:/avrdbg_run.log
logging.channels.c2.formatter = f
Now start studio and you should be able to see the logs in c:/avrdbg_run.log.
Hope this helps.