The installer hasn't "just" overwritten your file, it also made a BACKUP, clearly named with current date/time and original name of the file so, you can get your edits back by restoring it.
However, if we add fixes to our AFCADs in the meantime, you might not get them.
Not that this has anything to do with the Live Update, it would be exactly the same with a regular scenery installer: it would overwrite any AFCAD just the same. The difference is the Live Update makes a backup, while with the regular installer you had to remember to do a backup before running it.
