So each individual symbol is on your artboard as expanded vectors? Even if duplicates? This is interesting. (At least the work hasn't been totally lost!)You can please tell us what version and OS. Also have you tried restarting your computer? If it has only been the last few days, maybe something just needs to be cleared when you restart.
So ... I tried all of the Etch-a-sketch<tm> techniques prior to posting but that didn't work.
What did work was based upon a hunch. I performed a Save as ... into a different file name and tested an add of a simple new symbol and save. I re-opened that file and it has been working for a the last few times I've checked.
I think now that maybe the file became corrupted. This is bad.
One symptom I noticed during the workflow session was that I couldn't add new symbols. Earlier during that same session I was able to add other symbols. That was when I quit and reloaded and noticed those prior symbols became expanded instead of linked.
Here are some other details which might help spot at what point the file became corrupted.
Windows 10 Pro version 1809 OS build 17763.1757
I was using GPU [ 20 GB ]. It's off now.
I have my E:\ drive as scratch disk. Plenty of space.
I had Cloud backup on. It's off now.
My file size is 90 MB. I have 100 steps in the history.
I'm basically working on a highly detailed hexagon style map with lots of symbol instances.