They should have been more diligent when purchasing their bass ... or be less heavy handed when playing it. The best you can do is set the expectation that the quality of your work depends on the factors determined by the materials of the bass.
How? If you buy a $700 fretless bass, are you going to think, ah, this will be a piece of junk in 5 years??? of course not. you think they built it properly.
I've owned $200 fretless basses that lasted for years without treatment. I've had expensive fretlesses that ended up with mild abrasions but still sounded and played great after many years. My main fretless (converted from fretted) was an Ibanez musician (old 70s one) with ebony board, and it lasted for years and years and years of hard playing daily, professionally, without issues until the end, when I'd finally worn some audible wear issues into the board. it was untreated.
Treating a good board should be fine, as noted.
treating a terrible board will not go well, it seems.
Question is really - why is there such junk wood going into fretless basses these days? OR is the OP actually having issues with the product he's using, or the application method?
You can't educate the public to not buy sire, yamaha, etc fretless basses - which should be just great. You also can't educate them not to play hard, or to use rounds - I slapped on fretless with rounds my entire career - only minor visible marks, nothing audible until, as noted, many many years on an untreaded ebony board, and even then it would have been repairable (but I just sold it instead).
It's gotta be an issue with wood, or the specific application or material being applied.
I'm really interested to hear a viable solution here! Great thread, OP!