I had on my very damaged Combat Armor Mark 2 and bought another from the Brotherhood o Steel Vendor to repair mine. The 3.5k was subtracted from my inventory and the weight added to my inventory making me overloaded. I couldn't find it in my inventory. For the hell of it I bought another set and this time it showed up and I used it to repair my original set. But i'm still out the caps and even worse the weight of this invisible set still counts against me.

I have had similar disconcerting problems with 9mm pistols and biker goggles and throwing spears and bandanas. Find an empty container and move the version you can see into the empty container; your unseen version should now show up. If you equip this version it will stay visible. When it was happening to me it, only the objects that were at condition of 100% were "disappearing." The Throwing Spears might be some weird stacking or other issue. Yep ... its strange; hopefully, this is your problem.

[edit - helmets with goggles changed to biker goggles]

Happens to me all of the time with throwing spears (probably because I have 50 and some glitch doesn't allow it to show), but haven't noticed it with anything else.

I had exactly the same thing happen from one of the merchants at 188 - bought a Combat Armor Mk2 and it didn't appear
in my inventory even though the caps were subtracted. IIRC it was at about 70percent condition and lost me a few thousand
caps.

Try this in the console. (The 22103=Empty Nuka-Cola bottle.)

player.additem 22103 1
player.removeitem 22103 ***

Were *** is the number difference your encumbrance is off. If it's off by 40, remove 40 bottles for example.

This is from an old Morrowind fix for this same issue.

It's just another bug, one time I have bought the same item 6 time to actually get it. Which costed me over 20k. Just make sure you save before do any trading.