I can sympathize! My dad and I rebuilt an old dodge over the past 3 or 4 years (still a long way top go) and we lost a lot of parts, some of them multiple times.
I live about 3 hours away from the project site so I'd travel over for the mid part of the week and return home on the weekends to try to salvage my marriage. When we disassembled anything we put all the fasteners in marked Ziplocs and took pictures etc. I also put the parts in a specific location any time we disassembled, cleaned or painted a part. Any wear item that would be replaced during reassembly went into an old parts box, just in case. Often times (no every time) while I was gone my dad would clean the shop, straighten things up, clean a few parts, wire wheel a handful of fasteners, etc. About half way through the disassembly process dad decided to pitch that box of old parts, ugh.
When we started prep for reassembly we could find nothing. All the fasteners had been mixed up during the wire brush / thread chasing step. Most of the medium sized parts had been squirreled away in the most random of places. I found stuff wrapped in plastic in the crawl space, wired to the rafters in the garage, in the undercarriage of a motorhome, in the trunk of any junk car sitting around - it was maddening. We spent days tracking down parts or assembling then disassembling then reassembling things because we finally tripped over a part we couldn't find. In a few cases I even bought a replacement because we couldn't find the original (AB may have been in cahoots with my dad). We now have a box of random fasteners in a box on the shelf and a bunch of modern mismatched fasteners on the car, ugh.
So next time........ I'm going to make a dedicated spot for parts as soon as they come off. Be very regimented in opening only 1 Ziploc at a time. ensuring nothing gets moved or misplaced. I bet I spend just as much time looking for lost parts.
I certainly enjoyed this time with the old man, some day he won't be here to grumble at for losing a part.