Updated: Persisting without mods

TL;DR: The Nether and End are innaccessible, can't be found in default namespace

Before I downloaded the 1.17 server jar, I backed up server files as usual, then moved the 1.16.5 jar out of the server folder, placing the 1.17 jar in it's place with the exact same file name. I also updated two simple data packs I've used for a long time, changing the version to "7" instead of "6" and using this site to ensure there were no syntax errors across the total of two .json files in the two between the two packs, and that they were using syntax for 1.17. Upon using the same execution command to run the jar, I noticed it was taking much longer than usual to boot up and giving strange errors/warnings. When I tried to login, I couldn't and after a while, the server crashed, forcing me to reboot it.

After a reboot, I was able to login, but upon trying to enter a Nether portal, I was unable to enter the Nether; it hung on the portal animation for far too long. To test, I tried using /execute in to pull up the dimensions the game could see, confirming my suspicion that the Nether and End were gone. The only dimensions listed as suggestions in the IDE are the Overworld and my custom Skyblock dimension.

I checked to ensure that the DIM1 and DIM-1 folders still exist, and they do. Also used NBTExplorer while after stopping the server to look at level.dat, and it looks like the Nether and the End aren't even listed as dimensions in level.dat

Attached are a copy-pasted log showing the console during boot, another text file showing console during login, a screenshot showing the DIM files are still there, a snip of level.dat, and a screenshot showing that the IDE won't autofill Nether or End.