After the most recent update all my memorized bills and auto-entry transactions disappeared. I'm now on version R53.16, Build 27.1.53.16
I assume I just have to accept the data loss and manually rebuild everything?
Sometimes a version update causes unusual behavior giving the perception that data is lost or missing. It might be the case that it actually is but often it is not.
If you have not already done so since you did the version update, close Quicken and reboot your computer. Then check to see if the issue is resolved.
If it is not resolved, it might be easiest to restore the last backup file from just before the version update. Quicken makes an automatic backup file when doing a version update and saves it to the location where your automatic back up files are saved.
Another option to consider taking if these things did not resolve the issue is to uninstall Quicken and then download and install a fresh copy of the installation file from https://www.quicken.com/support/how-do-i-download-quicken-quickencom-after-i-buy-it.
Let me know if any of these things resolved the issue for you or not.