Short answer: Save to a new file and keep the old file as a backup.
Longer version: This "forced" Save As only occurs when the Muse file format has changed due to an update, or when Muse recovers unsaved changes following a crash, forced quit or power outage. It's our subtle way of encouraging you to create a backup copy at major transition points (file format change) or following a crash. Muse does not support "saving back" or exporting to a prior version, so if you need to share the file with someone else who's using a prior version or for any reason revert to the prior version of Muse, you'd need the file in the older file format.
If you already use an automated backup system and/or store your .muse file in a cloud synchronized folder, then keeping the extra copy isn't necessary, since these mechanisms would provide an alternate means to revert to an earlier version of the file, if the need ever arises.