what im not understanding is even though ive removed these from my vam folder they are still popping up when i drop the updated version on the hub even though they no longer exist in my save or vam folder, if i drop this var in my fresh install then build the package would that fix this or just bring the problems over?
Maybe try dnGrep
https://dngrep.github.io/ - with that, you can search your whole installation for every reference to a particular morph. And get a good editor: Notepad++ or VSCode are good. In DnGrep, go to Settings > Options > Custom Editor > enter Path to your Editor. Now you can double-click on lines in the search results and your text editor will open the file in question at just that line.
Point dnGrep at the folder you want to search, then search for one package (like eg "WeebU.AltFuta-gina."). (Fiddle a bit with the options - like eg. set search depth to 10 or so, allow it search archives etcectc.)
It'll show you all files where it finds "WeebU.AltFuta-gina.", and it'll show you the line where it finds "WeebU.AltFuta-gina." (Might have to "uncollapse/unfold" the search results if you just see the filenames). Now double click that line. You'll see something like "WeebU.AltFuta-gina.latest:/Custom/Atom/Person/Morphs/blablabla/BiggusDickus.vmi". Then you know that "BiggusDickus" is the morph your scene is using - that is the reason that package is being referenced. Now you can look for an alternative source for "BiggusDickus" - most likely source is WeebUR's morphpacks (here on the Hub somewhere). Or you decide that BiggusDickus can go f**k himself, and you zero out that morph.
Why look for an alternative source/morphpack? Because what your scene is most likely referencing is a presentation scene - a scene with another 20 dependencies of its own.
Scenes are bad as sources. What you want is a morphpack - morphpacks mostly have
zero dependencies.
Or maybe it's a humdrum ordinary morph like "Nipple Length" or something - loads of people have packages with duplicates from built-in morphs, or morphs contained in common-, Hub-hosted morphpacks like "Spacedog.Import_Reloaded_Lite." or "AshAuryn.Sexpression". Why? Because people are idiots - they unzip morphpacks into their install, forget about them, make some look or scene, and then the unzipped morph gets packed into that scene. Back before the .var system, that was common, so lots of older packages (wolverine333 etc) are built like that. Other possibility is that their scene is referencing such an old, messy, package full of duplicates.
The important thing is that you likely have a (good) duplicate of those ordinary morphs somewhere on your installation - so you can try just removing the offending package and checking whether VaM finds an alternative. One quick way to check that is to point DnGrep to "[VaM_ROOT]\Cache\PackageJSON\" and search for the morph in question - that's where VaM keeps a list of all the morphs it knows about.
It's not an exact science, you have to look a bit. And
read the guide posted above. I don't build scenes, I'm just handy with an editor and search tool.
TL;DR:
1) Morphpacks as sources instead of scenes -> that way you get the damn sub dependencies down. Scenes = BAD, Morphpacks = GOOD
2) Get an editor and DnGrep - makes searching much faster, and you can search ALL files in your installation simultaneously.
3) Read the guide.