[QUOTE=wtw1936;1710870]Using software to sync folders across our two computers, I share my library with my wife by syncing our Calibre library folders. If, for example, I create a user-column "Read" to indicate whether a book has been read or not, she and I can use the column, but when I update her folder all her Read info is lost and replaced by mine. Is there any way that she can retain her personal changes such that my updates won't destroy those changes?[/QUOTE
NO

you are using 3rd party programs to mess with Calibre's Library folder and they have no clue how to maintain DB integrity.
If done Carefully <- <-
You can save your changed books to a second Library (on a thumb drive or A blank folder on her system).
After you are done and give the OK, she can switch to the New Library and merge .
BTW Each of you need a Uniquely named custom columns for your read status or the merge overwrites. (and her column name can't exist on your machine or the status will be clobbered when merged) OTOH a Tag (read) column, Tags do get merged

(Jane, Steve, Dick)