FWIW, I have not seen this behavior with Sigil 0.4.2. I modify the content.opf both by adding files to the epub (e.g. cover image) and by directly editing the metadata section and the guide section. Sigil WILL tidy up the "pretty printing" of the content.opf (indenting the manually entered entries, for example) but so far I have not caught it undoing edits.
Edited to add, this is the Sigil 0.4.2 release installed on Debian Sid Linux.