Hard to say without really seeing the fixture/LED, but if you end up going the epoxy route, I'd use a thermal epoxy to be sure about the heat concerns (lower die temp will be longer lifetime), and then maybe try to develop a jig or something to hold them in place. With lots to do, you're going to lose most of your time redoing them waiting for the epoxy to get tacky enough that you can leave it be, so having something to hold/press it in place could be useful in speeding things up.
Alternatively, if the LED module can be screw mounted, you could look for a way to drive the screws into the existing housing (drill and self tappers if there's a spare layer before you get to the outside), or maybe find something that could serve as a mounting bracket/plate. For example, if you could epoxy your plate in place or otherwise affix it that way, you could come back and screw in the LED module - could simplify attaching wires, make it possible to replace the LED module itself, or just make the mounting depth better.
Since these are retrofits, if they were incandescents before, you may find that an LED module sits too deep in the fixture, which gives the light a narrower beam (and any LED optics could do this on their own), so having the LED a little farther from the back wall could end up being better lighting for your situation.