How tough a job to remove and replace caulking on a glass roof?

Not so bad, just tedious. Get a 'painter's tool' and it helps when cutting the old caulk out of tight places and will scrape the wider joints as well. Fiberglass is so much easier than rubber!
I cleaned the joint on the side/roof with Windex and dried it thoroughly before applying the caulk from Winnebago factory store. Then used the edge of the tool to even the surface of the caulk.
Being a bit over-thorough I went back with Ebond on the joints simply because I never wanted to go through all the ladder moving and climbing again.

I just had it done by an "on-site" RV tech who came to my storage garage. He used a heat gun and broadknife (scraper blade) to loosen the old stuff and scrape it off. He then wiped it down with a solvent of some kind, let it dry, then applied new caulking with a regular caulking gun. Walking around on my crowned roof is not something I do real well any more, so decided not to tackle it myself.

Not real high tech, but it took him two days to strip and reseal everything, including front and rear caps, but excluding the roof edge seal. He says they are not usually a problem, which I accepted at the time. The more I think of it, the less sense it makes to me. Why would the roof/wall seal not be critical? I'm going to start another thread, see if I can find out.

My coach is older, has the EPDM roof, but penetrations still have to be caulked, regardless of the type of roof material.

Good luck.