Instead of decrypting the PS3's executable and patching it manually, you can instead make use of RPCS3's patch function. There's information on how to set the file up on the RPCS3 wiki. This will save time for the end user as it won't have to recompile the executable every time and will instead recompile the edited portion of the executable.

It's also worth mentioning that RPCS3 allows you to decrypt the executable, it's under Utilities -> Decrypt PS3 Binaries

Looking into RsdxPackedCacheFile.bin, it looks like it's just a cache for arl files in the game. This will cause conflicts to occur with any new file additions within an ar file.

I was installing the Episode Blaze mod and this happened

This happened after clicking the 1 click install button in the gamebanana page, so idk what to do.

Some mods (ex. No HUD) will modify a file in an archive that is commonly modified (ex. character mods). An option to merge the mods together (like ARC merging in Sonic 06 Mod Manager) would help out with a scenario like this.