i have the same problem. i switch from the fretted to the fretless for 2-3 songs and then back to the fretted....
(i could get a switcher and have both active-electronic basses plugged in at the same time, but the fretless will just sit there plugged in and draining the battery 90% of the practice time.).
the boss tuner should mute the signal when unplugging/plugging the basses; but it does not.
i run everything through a pedal power 2; no batteries in any of the effect pedals.
i use eminence gold cables between all the pedals, mogami and monster bass cables for the basses and 2 amps.
(the bass runs through boss tuner, boss limiter (for slapping), compressor (for tapping and some disco songs), eq (i use it as a boost when i need to be louder and depending on the acoustics of the venue), and then a splitter; one going to the 250w amp (expandable to 500w); and the other to the 100w amp (expandable to 200w) for the effects.
i am in a effects heavy band with only 1 guitarist so i bi-amp my signal to a "clean" signal and an effect-heavy signal so it sounds like there's 2 players up on stage. the effects-heavy signal contains a pog, fuzz, distortion, overdrive, chorus, and delay and flanger.).
my electrician friend suggested that it since i'm in an old building it may be a grounding or wall outlet issue in the building; so he suggested to get a expensive surge protector that may solve the problem...
i just ordered it so i will let you know of the results later on in the week.
i may lag on a post. so you can always reach out to me on
exaxrxlx@gmail.com
just in case i lag on a post....