I haven't read it yet, but doesn't the Marvel comic Star Trek: Untold Voyages make the case that the original Marvel run was part of a "new ongoing mission" between TMP and TWOK? I was told that aside from some wonkiness about setting up TWOK elements a few years earlier than it should, it seems to work fairly well as "bridging" the Second Five-Year Mission concept.
^Uhh, the original 1980 Marvel run was explicitly presented as a new ongoing mission after TMP. There was no need to retcon that later; it was overtly the case from the beginning. Just about every post-TMP novel or comic since then has been, has had
to be, in a post-TMP ongoing mission, so it was hardly an innovation for Untold Voyages
to follow that established precedent. And UV didn't reference the 1980 run in any way, as far as I recall. The '80 run wasn't that well-regarded, and I doubt Marvel was eager to remind people of it.
Maybe what you're thinking of is the cover to UV #1, which had the caption "Tales from the Second Five-Year Mission!" But that was far from the first mention of a post-TMP 5-year mission; for instance, The Captain's Daughter
had mentioned it three years before UV #1 came out, and I'm sure there were earlier references as well.