Absolutely there have been tunes where the "boyz" have changed keys after the song "melded" for a few years....
Bird Song, absolutely early ones were in D. Very different feel to those and cool in it's own way. I much prefer the E version though. I could be wrong, but wasn't every Birdsong pre '75 hiatus in D? Then it never came back until the Fall '80 acoustic shows which was when the "E" started.
I just preferred the airy, spacy trip the E versions got to, more than the angular, sharp D versions. The D versions heavily leaned on the Dominant 7. The later E versions had a much jazzier, modal theme.
Brokedown Palace is another one that got the key change post hiatus. Brokedown is an example of a tune where I LOVE both versions. (Usually I have a notable, strong preference on songs that have been "changed" one way or another)..... Both versions were so cool. The 80's version were so moving and Jerry's solo rarely failed to disappoint. The key change and structure gave it such a nice spiritual setting. But the early 70's versions with the "Do Do Do's" at the end carried its own ultra cool vibe!
My thing with key changes (and really specifically with Dead tunes) is that tunes are written in certain keys for a reason. Different Keys just carry a different vibe to them.
Would Scarlet be Scarlet without the "B"?! It is such a bright, Caribbean lilt, and the Key gives it that feeling, it just doesnt sound right in other keys to me.
How could China Doll start on anything but D min?! (the saddest of all Keys, Thanks to Nigel Tufnel).
I loved the openness and exploration of the early 2000 Phil and Friends lineups, but man did some of those transpositions drive me NUTS.
.......................................................have you heard the one about the yellow dog?