I don't care if the guitar is on the left or on the right
the technical question is if the sound quality may be changed because of the mix (sound stage, details, ....)
Well, it is hard to answer your question without at least being mistaken as ironic. I suggest to connect the left speaker to the left output and the right speaker to the right output. Might be of help for classical recordings, where the placement of the orchestra follows certain rules.
I could only imagine the SQ to be altered when for example one speaker is located near a corner or a sidewall and after the swap it has to reproduce some signals which were located on the other speaker before. And due to the not optimal placement it might effect the overall SQ.
But this is an academic question really: just connect the speakers as intended in stereo (right and left) and call it a day.