Hey I've had this issue in the past (before this update). VCOM in its current iteration (2.94) is the problem. I fixed it and still was able to use VCOM by pulling the most up-to-date VCOM version from their github and running the script version only on my server. Pull the VCOM assets, place them in your mission folder with mission.sqm with [] execVM "VCOMAI\init.sqf"; in your init.sqf in the folder to enable VCOM.
Before I did this, running either the modded version or scripted version, saving was iffy. The memory leaks from the current VCOM make it nearly unusable.
After this, my missions save just as quickly and as thoroughly if the server has been running a mission for 5 minutes or 5 hours. No more hang-time until the server just crashes trying to do a server save and exit after running an operation -- and you still get to use VCOM! Everyone wins!
This doesn't require you to run VCOM as a mod either server-side or client-side. Until the memory leaks are patched on the official VCOM release, this is the best fix.