Changing mods in Aemulus doesn't affect the actual game (Persona 3 Portable, PPSSPP)

[agile cove]

A few weeks ago, I started up a playthrough of p3p, with some mods installed. I doubt the specific mods themselves are neccessary, but just in case here's all the ones I has when I first started my playthrough. I installed all of them on GameBanana using the 1-click install with Aemulus.
At first, all the mods loaded perfectly, but I'm running into a major issue now. I recently tried to install the mod menu (https://gamebanana.com/mods/174390), but when I opened the game it didn't work. I thought it might've been conflicting with another mod, so I gave it higher priority. When that still didn't work, I deleted all my mods except for the mod menu. Not only did the mod menu still not show up, but the mods I had supposedly deleted were all still active. The modded logo (https://gamebanana.com/mods/286383) that I later installed didn't work either.
I've done everything I can think of to try and solve this, but nothing has worked. Nothing's installed in OneDrive, I've made sure that all the paths are outputting to the right place, I've both unpacked the base files and built the package several times, I tried uninstalling and reinstalling the cheats folder, I put the .iso for p3p in PPSSPP/PSP/GAME, but the same supposedly deleted mods are still there. The only way I've found to get rid of them is to disable cheats within the PPSSPP menu, but I obviously can't use the mod menu if cheats are disabled. The only thing I haven't tried is uninstalling PPSSPP, but I'm unsure if that'll delete all my save data, and I can't find a clear answer for that online.
I checked AemulusPackageManagerv6.4.0/Packages/Persona 3 Portable, and the only things in there were the modded logo and the mod menu, so I believe the problem is the .iso somehow stopped getting updated by Aemulus. I didn't change any settings in Aemulus between starting my playthrough and now.
Any and all help would greatly be appreciated, thank you in advance!

[keen crater]

@agile cove just to be sure... you are rebuilding mods every time you change things, right?

[agile cove]

Yes, I am

[agile cove]

I've looked into the problem a little more, and it might be that I installed the full version of PPSSPP instead of the portable one. However, I have no idea if uninstalling PPSSPP will delete my save data. Does anyone know if uninstalling and reinstalling PPSSPP will delete my save data, and if it does, could I potentially carry over my save data from one version to the other?

[foggy yarrow]

C:\Users\username\Documents\PPSSPP\PSP\SAVEDATA is the default location, or locate whatever folder it's installed to, ones starting with ULUS10512 should be your save data

[agile cove]

Thank you!

[agile cove]

Okay, so after I uninstalled and reinstalled PPSSPP, this time making sure it was the portable version, reconfiguring all my paths in Aemulus, and reinstalling both the .iso and the mod.cpk just to make sure, it still didn't work. However, this time I noticed this error message after trying to build my package:

I don't remember if that was there before

There are no other error messages in the log that I could find, so I have no idea what's wrong here

According to this guide, all of my paths are correct https://gamebanana.com/tuts/14001

Here are all my paths