I do not like parts and pieces for MOD's (Thinking as a user), keep it simple to reduce ambiguity on the users part.
So, any time I update, I'd replace the whole MOD file and note the version on its ZIP and prominently in description
and remove the old version (there is no reason to maintain the old version on the Nexus servers)
Now I understand a big MOD, over 100 meg being a pain to down load everytime a update (multiple times) happens
and Authors tendency to just perhaps put multiple patches up ...Unless it is an emergency update (then patch file),
I'd wait until an update has accumulated a number of fixes/enhancements then once again, replace the whole MOD file.
I think a good general rule is that even 150 meg MOD only takes the normal user maybe 3.6 mins to download, thats
no so bad as to REALLY consider patching over replacing because of download time.
In so far as your particular problem, AS LONG AS YOU KEPT THE ORIGINAL CONTAINER OBJECT, I do not see any
reason for corruption of user items within.