That seems like the DOL file was nor properly replaced.
Check that you replaced the original game's main.dol file with the Redux DOL, should be called "redux.dol, rename it to "main.dol" and replace the one from the original.
If you want to avoid any cutscene/story changes, then do not use any of the movie, bgm, message folders.
Simply use the model and the DOL/REL files, that should give you all the visual improvements and none of the modified story.
Yeah Hard mode doesn't have Missile Expansions, not even Energy Tanks nor Accel Charges
Hard mode forces you stay with the minimum/starting missile number, as well as initial charging speed and initial health, so you have to rely on concentration...
you need to generate prelit flats and use a special converter at this point. i will soon release it. the prelit flats and differnt codebase probably broke those legacy steps
The final two cutscenes are now uploaded into the Archive.org page and the Github repository as well.
The hack should now be complete, if you want to, you can go ahead and make the XDelta patch for the hack. It should work over the US/JP version.
From my several tests, I found two more SFD cutscenes that would still need a recolour:
dm57_cut06cto07.sfd - Brief right after Ridley is attacked by the Queen, which shows a closeup of Samus in her Varia Suit, lasts only like 2-3 seconds but...
The new file is redux.rel, it's only in the Github and Gitflic repositories right now.
I kinda... forgot to add everything to the Archive.org link lol
But shouldn't be that hard to do, I'll add that tomorrow.
I had wanted to make an xdelta patch that could be much more simply applied to the game. I made a sort of "beta" one a few years ago that worked great in terms of ease-of-applying, but it wasn't complete since it was in the middle of various...
Nice to finally have a good version of this game with watchable cutscenes.
Now to wait two decades until someone fixes Metroid Prime 3 that's noy bad but could be better.