Keep losing/misplacing audio files

I know stuff like this has been posted before as I’ve read some of the articles but I’m still a bit confused.
I never had this issue in 10+ years of using Cubase, but recently I’m opening projects (usually recent ones but not only) and I have a ton of missing files. The audio is not there, or in some cases, it’s been replaced with entirely the wrong audio. E.g a project from last year had a load of files I recorded recently instead of the ones that should be there.

I always create new folders everytime I work on a new project, but it seems that some of these don’t have an audio folder. A bunch of things are ending up in some random folder that I haven’t used for 3 years.
I read that it could be to do with templates? I always use templates and this was never a problem. Can someone explain to me the correct process to use templates without having this really irritating problem having, and causing me to lose a ton of work or render my projects somewhat useless as I need to redo half the stuff in there.

Note that I understand I have most likely deleted the files I want. I always empty trash in my pool because they’re supposed to be files that aren’t being used!! I don’t understand how it’s telling me files are trash when they’re obviously being used in a project.
So I don’t expect to get any of those back unfortunately, I just want to fix this bullshit and stop it happening to me again because this is ridiculous.

I don’t know what I’m now doing differently that is making this happen to me. It’s a real motivation killer when you start to work on something and then lose half the work you’ve done or can’t find it.