It depend. As an example:
I modded my 1984 MIJ Fender Jazz Special, so it is more useable. I had this bass since 2001 - 25 years , The Fender pickups were hot but also muddy like those hot Duncans that have zero sparkle and the electronics and TBX tone control sucked and the bridge bothered my palm muting besides it wasn't stable. So GZR pickups, added a parallel mode via push pull, a usueable tone control, Hipshot Bridge, De-tuner on E, Reso-lites without adding new holes and Tusq nut. The neck was already a nice specimen of subtle flamed maple and the rosewood is dark. Now a usable PJ and doesn't look that different except for the bridge and knobs, I am even removing the paint on the EMG logo.
All mods improved the bass a lot. It has painted bass body in solid color and I am keeping it that way so that it keeps its modest appearance. Better than any American or even custom shop Fender passive PJ in sound and playability and it is also light.
I am not going to reverse any of the mods -- if I will sell it. I will give all the parts. But if you are a player, there is not need to go back to the original parts -- if you are a collector, you are not the buyer I seek,
MY Pedulla Buzz had issues with the J pickup and I got a replacement from Bartolini, but as I ordered it, I had this impulse to get EMG X series preamp and Alnico pickups and the BTS EQ was better than the 2 band Bartolini , This is a 1989 bass. If I will sell it, I will revert it and use or sell the EMG items , because I actually have the spec sheet for it that says it has Bartolini and that is something that adds value. So I am keeping all the pickups and electronic packed well in the event I will sell it. The bass will not benefit from upgrading bridge, nut or tuners, I do feel the EMG was a worthy mod to me as a player but not as dramatic as the Fender above.
Having said, I am not selling these two.