I think you could have got yourself out of trouble if you had a proper timecode in your files. Exporting the timeline as an EDL, reimporting it without medias and specifying the audio folder only in you media pool might have been a workaround (maybe editing by hand the EDL file in the process) but doable. However, if I got this right, it won't work for you... You mentioned "Auto-sync audio based on waveform" ? I assume that implies the audio TC does not match the video TC ?
AFAIK, Resolve can't autosync within a timeline, you have to do it in the mediapool and indeed, that will affect the master clips but not their previous usage...
Two Ideas come into my mind :
The tedious manual way : write down Begin TC and End TC of each clip in your timeline, and rebuild a new timeline from your now complete synced master clips.
The third party way : Adobe Premiere can autosync clips in a timeline, one clip at a time (1 linked audio/video + n audio tracks).
You could either spread the clips appart to give room for the full audio lenght, sync, trim the audio and put the timeline back together, or you could stack the audio clips giving them one track per clip and then trimming the audio tracks to corresponding clips above.
Alternatively, Red Giant sells a software that can perform those tasks in a more automated way : Plural Eyes, it should work as long as you give each clip a separate pair of audio tracks to move along.
Either way, it's going to take a lot of work... From my experience, what seems tedious at first (manually doing the job, one clip a time) generally ends up being the shortest solution. Digging into new softwares and workflows is generally time consuming on itself and if it is a one time fix, you'll probably find out that it was just not worth the effort. Actually, you'd probably be done with your timeline by now if you had begun working on it instead of asking for help in this forum!
If the effort turns out to be useful in the future it might be worth it, but in your case, frankly the lesson is : DO NOT START THE EDIT BEFORE SYNCING !