Our dodger was, indeed, well bedded to the deck. I'm sure everyone's is - it's the "AMEL Way". What I did was to VERY carefully, using a fish filleting knife, insert it under the dodger to cut the caulk. That is a CAPITAL LETTERS VERY CAREFULLY! You may come up a better tool but it must be very sharp, very thin and very strong.
First though, I rigged a line to a halyard with some snatch blocks to the mizzen to make it lift straight up from the dodger, then led it through the windshield opening window and applied a LOT of lifting force. Then I went to the filet knife and started cutting. After a while I saw some movement and then used some chisels as wedges to break the seal more and it finally worked. I had three tiny nicks (about 1/8th inch roundish) in the deck gelcoat at some places in the base of the dodger where I was not careful enough with the chisel. I patched them and they are not visible now. This took about 3 hours to do. You should take 4 hours and not nick the gelcoat at all.
Once the dodger popped free it is easy-peasy. There is wire through the deck in the middle of the dodger going to the overhead light but it has enough slack (about 6 inches) so you can easily tilt and swing the dodger to allow the companionway hatch to slide up and out. Re-bedding was very easy. I just used silicone so if I need to take it off again it will be easy, but you can take your pick of bedding compounds.
If I recall correctly, I did this about 2004 and the Plexiglas (Perspex in Europe?) is still in excellent condition. It does have a couple of barely noticeable vertical scratches where I must have been careless with not cleaning off some boatyard grit, but, it's hardly noticeable and hey, we're talking 15 years!.
The one thing that isn't perfect is that I chose a plexiglass with a very light grey tint that seemed like a good idea at the time. That's great, as during the day it looks like a black mirror from the outside, giving complete privacy below - at night with lights on below you can see right through, hence the hanging privacy shade. During the day, though, if the hatch is closed and exposed to direct sunlight it heats up and expands such that it binds in the track and is hard to open or close. Just a small annoyance, but if I did it again I might choose totally clear plexiglass and maybe a fraction thinner. Or, and it's one of those "one-of-these-years" things, I might just sand the wood slots a bit wider but, obviously, it's not a big deal. We've got a great "T-Top" over the cockpit so sun on the plexiglass is rare.
Katherine and I think it is one of the best modifications we made to the boat and we did not do it until we had lived aboard for 5 years, so we did think it out thoroughly. Then, after we did it we hired a psychic who put us in touch with "The Captain" - the psychic said that he was smiling! That's our story and we're stickin' to it!