Converting to text only is akin to throwing the baby out with the bathwater.
The bookmarks are not a particular problem you need to remove and certainly if there are any cross-references in the document, removing bookmarks could be causing lots of broken cross-references.
You can HIDE the bookmark indicator so they become invisible by going to Tools > Options > Advanced > Show Document Content > Show Bookmarks and unchecking the box.
You can delete all bookmarks by running a macro such as
Code:
Sub KillBookmarks()
Do While ActiveDocument.Bookmarks.Count > 0
ActiveDocument.Bookmarks(1).Delete
Loop
End Sub