I'm working on making my own custom hood, and I just ran hoodchecker to see if there's anything funky. Here's what it came up with:

"User File Warnings:
Sim has no Character file: 0x004E SimID=0x008AB403
Sim has no Character file: 0x004F SimID=0x008AB402
Sim has no Character file: 0x0050 SimID=0x008AB401
Sim has no Character file: 0x0051 SimID=0x008AB400

Family Ties:

Sim Relations:
Sim does not exist: 0x02FD has relationship with self
Sim does not exist: 0x02DA has relationship with self
Sim does not exist: 0x02FE has relationship with self
Sim does not exist: 0x0214 has relationship with self
Sim does not exist: 0x02F1 has relationship with self
Sim does not exist: 0x035E has relationship with self
Sim does not exist: 0x0211 has relationship with self
First sim does not exist: 0x02DA has relationship with 0x0020 Olivia Walton
First sim does not exist: 0x02DA has relationship with 0x0021 Quinn Walton

Sim Wants and Fears:

Memories:"

Olivia and Quinn Walton are both living sims. I opened up SimPE to check, and sure enough there are 4 unlinked, uneditable character files. I have no clue how they got there, or what they're from. I haven't deleted any sims, and I went and checked and all of the ancestral dead sims that I have made are all accounted for, so it's not any of them being corrupted. I checked Quinn Walton's relations in SimPE, and there is no unlinked character (though there are a lot of auto generated npc pets and sims showing up that he has not met in game, unless I just wasn't paying attention while setting things up and he was talking to every single walkby.) I also have no clue who or what the sims referenced in "sim relations" are, as they have no name in hoodchecker, and there are only the 4 unlinked character files showing in simPE.

While digging through SimPE, I just noticed that the 2 most recently created/killed ancestral sims have relations towards all the bad NPCS (The therapist, Remote Control, PT, Rod Humble, etc), however none of the other ancestral sims (or living sims) have any ties to these NPCs, and I didn't do anything weird with these two, I killed them via old age with the tombstone of L+D within 5 minutes of moving them in to the household with their living daughter, which is what I did for every other ancestral sim.

Is there anything I can do to fix this? Or do I just need to start over? If that's the case, what can I do to avoid this happening again? I'll be doing a fresh install of the sims 2 if I do need to restart my custom hood. I have no CC, just mods like sim blender installed currently.

Unlinked character file is different than no character file. You probably just have a multi-PT hack installed, or something.

Oh that's probably it, I did have a 4 pt multi pt mod installed, but I removed the file that makes them into PTs. So otherwise it should be fine? Or is this likely to lead to corruption?

I don't know what you mean by "the file that makes them into PTs". If you just mean the file that chooses them to be the alien parent, that doesn't prevent them from being in your hood, no. Any neighborhood you load with the character files in your downloads folder will have those sims in it. If you want to make a custom hood and don't intend to redistribute those PTs and all their genetics with your hood, you will have to take those character files out first.

The PT mod has their character files, and then a 5th file which directs the game to use them as the default PTs. To be safe, I'll do a fresh install of my game and start over on my hood, and won't reinstall the PT mod until I'm done it. Thanks!

You don't need to reinstall your game, just take the character files out of your downloads folder while you work on your custom hood.

Reinstalling is for issues in the install, the download folder and hoods are under My Documents, separate area.
Try right clicking the sims 2 folder and adding a word to the end and load the game to make yourself a fresh folder. You will need to make a download folder for the new folder, there are no PT or other NPC mods in that. It's vanilla.

Simply rename the folder you wish to play the same name it came with and make sure the folder you don't want to play has a word added on the end of the name. The game can only read the correctly called folder. If you have the small TM symbol in the name its important to keep that.

I'll do that, thanks!

That will save me a lot of time haha, thank you!

If you make a second folder you don't have to remove anything. You can have as many separate sims 2 folders as your pc can handle. I have several.
Just be careful on the renaming and check and see if you have the TM symbol. If you do and you remove it you can't get it back easily.

So I wound up starting the hood over again (I wanted to make changes to the .sc4 terrain) and copied the sim appearances via simPE, and suddenly I'm getting the same 'sim relation' errors in hoodchecker (it was fine yesterday, and I did the same thing as I was doing last night so I'm not sure what I did to cause this again) but is this an issue?

Sim Relations:
Sim does not exist: 0x01DB has relationship with self
First sim does not exist: 0x037A has relationship with 0x0026 Melissa Sommer
First sim does not exist: 0x0124 has relationship with 0x0026 Melissa Sommer
Sim does not exist: 0x0377 has relationship with self
Sim does not exist: 0x0124 has relationship with self
Sim does not exist: 0x01F3 has relationship with self
Sim does not exist: 0x01EF has relationship with self
Sim does not exist: 0x01C5 has relationship with self
Sim does not exist: 0x037A has relationship with self
Sim does not exist: 0x01E5 has relationship with self
Sim does not exist: 0x01F6 has relationship with self

There aren't any other issues, just these, but I have no clue where they're coming from or what's causing them, or if I should even be concerned about it