FreeFallup2295: I've run into the same issue as well. I've found it's possible to progress if rolling back the version number to 1.0 from an install through Galaxy. The game does seem to have more visual glitches & oddities at points buggier in this state, but the warp bug seems nonexistent in that version. I dunno if there's a way to roll back the version without Galaxy tho.
Going back to v1.04m while trying to load from the second area just boots you back to the menu endlessly at each attempt. Using red stone warps from the alchemist to the second area in v1.04m (from a 1.0 save) just causes endless loading. As far as I can tell, attempting to warp to anywhere directly connected to the second area physically in v1.04m after reaching it in v1.0 doesn't work. All warps unconnected to it (at least in the first area, as I haven't yet gotten to the second main page boss to confirm either way). That being said, you can warp to area 1 & progress anywhere that doesn't require warping into the second area (such as the mansion once you have the key).
TLDR; roll back to version v1.0 & you should be able to progress. Only revert to v1.04m when you're certain you can make progress without warping.
EDIT: Okay, just beat the second page, was warped to a new location. Updated to v1.04, tried loading save, infinite loading as before. Reverted to v1.0, game loaded fine. Better off just keeping the game at v1.0 to be able to finish it atm. Hopefully the devs release a fix soon so the game can be completed at the current version. Still, should be completable at v1.0
Also a note: when reverted to v1.0, the title screen still lists it as v1.04m, even though it is not.
Man, thanks for the tip! I wouldn't have thought to try this, otherwise. At least I can continue playing now.