Old thread, still happening, and for what it’s worth, I’m only even using independent time signatures in this project because it’s the only way I can see to have a slash region with 3 quarter notes instead of 2 dotted quarters in 6/8 time.
Someone here found what seems to be a solution: if you add an ossia on one of the staves with an independent time signature, the rehearsal marks reappear — and they stay even after you delete the ossia. I just tried it and it seems to work! I’ll look for the original post.
I found the post, credits to @Wim_Hoogewerf!
Wild. I’m having trouble figuring out why an ossia staff would cause Dorico to recalculate the bar numbers, but whatever works, I guess!