I ran my custom hood in progress through hoodchecker, and the only thing popping up is invalid relationships. (Ie, sim a and b do not exist and they both have relations with eachother, or sim a has relation with self, etc etc) I see all these invalid relations in SimPE, and while I'm not even certain that's necessary for me to resolve these issues, I'd like to know if I should and if it's safe to just delete them in SimPE, or if that's a bad idea. I've tried searching all over for an answer to this but I can't find anyone clearly stating if deleting sim relations is safe to do.

Take my advice with a grain of salt, but I seem to recall Hoodchecker fixing those with the "Remove" function. That, or they're not that harmful in terms of removing them. From what I remember they're really common in Sims 2 neighborhoods.

I don't think you have to delete that stuff. I don't personally use HoodChecker anymore because it can in rare occurrences damage the neighborhood. I don't believe the SRELs and memories it typically reports on are actually problems, technically it will tell you if there's a missing character file, but it identifies custom NPCs as having missing character files and I think if you actually deleted a character file you would know about it anyway.

Okay, thanks! I'll just leave it then, since I'm certain I didn't delete any sims.

And you didn't remove any NPC creating mods? For example a multi alien pollination set or a one off NPC like Beks rideable animals or the surfing mod?

HoodChecker can't detect whether or not custom NPCs are installed or have been removed, and this person wasn't even saying that HoodChecker was saying there were missing character files. I just mentioned it because it's the only thing I've seen HoodChecker report on that I think could potentially be a real problem, but like I said, if you've deleted character files you probably don't need HoodChecker to tell you that.