The pause button causes a lot of issue in this case and now I’m suspecting that in this and this issues I had, it was the same cause (at the beginning of setting up my new computer, I did a lot of moves, reallocation of folders, etc).
I give up to the many problems and I restart all insync related files, folders, etc and started a new and fresh insync installation, only using default locations. Now I have no problems related to (not)default, deleting, moving things around, unfortunately, this approach can’t be applied to your case.
Insync developers, could be a good idea to at least warm the user when it pauses the insync and it is doing some “maybe buged” operation?
Also, could this be reproduced shunting down inync, killing it, or just a computer freeze?, as this is something to worry about and to be very careful when doing some massive moving or operations. (all this while doing these conflicting operations)