iif qtractor is asking to save into a session filename of its own then, i guess you're probably using a way too old version of qtractor, even older then qjackctl's as jack-session manager altogether.
recent qtractor versions shouldn't ask for any session filename (.qt? suffix) when saving under a jack-session command context at all--UNLESS you're issuing a "Save and Quit" command and you have a scratch/untitled qtractor session going on--take note that this scenario is not exactly what you described, but ntl.
in either case, please never , i'll repeat NEVER tell qtractor to save its own session file onto the SAME location as ANY of the jack-session directories you've been dealing--instead, ignore or cancel the file requester dialog OR save that file somewhere else for your records ;)
yay. which qtractor version?
iif qtractor is asking to save into a session filename of its own then, i guess you're probably using a way too old version of qtractor, even older then qjackctl's as jack-session manager altogether.
recent qtractor versions shouldn't ask for any session filename (.qt? suffix) when saving under a jack-session command context at all--UNLESS you're issuing a "Save and Quit" command and you have a scratch/untitled qtractor session going on--take note that this scenario is not exactly what you described, but ntl.
in either case, please never , i'll repeat NEVER tell qtractor to save its own session file onto the SAME location as ANY of the jack-session directories you've been dealing--instead, ignore or cancel the file requester dialog OR save that file somewhere else for your records ;)
cheers