We have had problems losing new changes in the vault and double references in drawings and assembllies. Could the issuse be related binding read / write access to ownership?
If you aren't checking files out when you intend to change them, I can see this happening. But more information about what you are experiencing may be needed to give a more definitive answer.
Also, be sure you have "validate vault" turned on just to keep it up-to-date.
Also in the vault admin tool check to see how you have permissions
When you say you are losing changes in the vault, what does the history look like
for these files in the vault?
Retrieving data ...