IIRC the original bad rep of the 1895 with the '03 & '06 cartridges was due in at least some part to increasing headspace issues. Apparently this problem didn't happen with all rifles, only with some.
IMO you'll be fine as long as your smith ENSURES that the headspace is minimal in the beginning. To me this would mean that a rebore MUST have the barrel set back one thread in order to clean up the original chamber, not a big deal but still of some importance in my mind.
Additionally, I recall some sort of confusion about the actual headspace dimensions of the factory 35 Whelen back when it was legitimized; this may have been a brass issue rather than a chamber issue but IMO it's worthy of investigation.
Sounds like a worthwhile alteration, I wish you good luck with it!
Regards, Joe