Edit: After posting my answer, this seems to still apply albeit maybe for two different reasons. There are actually many possible scenarios that could result in the same issue.
After reading through the information about how their network optimization took place in this last patch I noticed a few similarities. First off, they reduced the size and attempted to only send information that was deemed "relevant to the client" (potential hazard A). Secondly, they reduced the frequency that clients received updates on certain items deemed "stationary" or unchanging. Thirdly and lastly from my perspective, this issue occurs "randomly" but seems to be happening most during periods of extensive building by a single client.
Now I don't work for Coffee table games, and I only know what I can see without looking into the code, but I suspect the issue has to do with either A, B or (most likely) a small combination of the two. Since the host (currently the server) always knows that the information is there, meaning he can see and delete said invisible structure, that means that the initial packet was sent and verified by the server. The fact that the clients can reconnect, also means that when the game loads, the information is in the server and is sent at startup.
Second, since the host can delete and either player can re-place the object, that also means that the check and update packets (now delayed by time) are no longer getting dropped. This used to occur because of the buffer overflow getting dropped due to bad netcode, but it seems now what is more likely is that some of these are just not getting included in the updated sync packets. This could be the result of both A and B if certain structures are only allowed to send their sync data every X seconds. Additionally, the replication state does not seem to be representing the structure updates. If the replication state takes place before the entirety of the data is sent, but is still sent in the same window, its possible that the update is just getting lost due to miniscule timing differences. Additionally, If you build more structures than the data allows, the buffer fills for the prepared scheduled sync packets and again you have buffer overload but for a different reason.
Just going to throw out a disclaimer, this is entirely speculation based on reading the article about what their network optimization patch did here: https://www.gamasutra.com/blogs/GafgarDavallius/20190718/346598/Satisfactory_Network_Optimizations.php
TL;DR - Chances are this has to do with the network optimization. I also want to throw out expectations for the fix - They are currently on summer break and likely so until the middle-end of August :-( ... but we can hope :-)!!