I logged in today and everyhing at my base is gone including all the things I have been storing up in my vaults. This is most concerning.

No surprise, the building stuff has been overworked and doubled. If you keep your old things this may clash with new features.
In videos on youtube I have seen guys keeping their stuff.
[EDIT] humm, their inventories in ship, exosuit, freighter, mulit-tool still all there , don't know exactly about farming products, but their homebases were also intact after loading foundation saves.
Probably it still goes that if you want to keep everytzhing from your base, you'd have to dismantle manually, a pain to do but you keep all.

XenonS

My base, along with the hydropontic growing bins, storage units and their contents, and all of the base elements (windows, etc.) all made the transition to the Pathfinder update intact. No problems there, so it's not a universal issue. I am running vanilla, no mods at all, if that makes a difference.

I do wish they had increased the limit on the allowed "complexity" in the standard base after adding the exocraft elements. I did need to disassemble some of the glitz (mostly windows) in order to have enough "complexity" units remaining to get started with the exocraft console and external pad.

i can now confirm that I have kept ALL my materials, my inventories and my homebase inclusive the farming. I went into my cubic room (farming) and everything still there and growed ready to pick up.

I completly have de-installed / re-installed NMS after backing up my saves, then started a new game just to write the new savegame folder, then replaced all with my backup savegames and important: deleting all shader caches.
I run very fine now, grafics much improved, my ship color has changed as well as cockpit interior, better lighter outside grafics and NPCs looking somewhat differently. No FPS drops, even after changing FOW to 100% (I play with medium settings, GTX 960, I could probably raise grafic settings but I will restrain for now because all is fine).

XenonS