Dropped items in space sometimes disappear immediately. Happened a couple times when removing warp engine parts and did not have enough room in my inventory. Happens with dropping stuff randomly.
This appears ok in the latest experimental release A11.5.5 B2774 if possible can you try it out on the experimental branch & check also ?
I have also had this happen. It is a pain when blocks just disappear. Its a good idea to turn on the connected toolbar to a cargo container(F4) when altering vehicles.