problem with Mail Rules disappearing

Give this a try: boot into Safe Mode according to How to use safe mode on your Mac and test to see if the problem persists. Reboot normally and test again.

NOTE 1: Safe Mode boot can take up to 3 - 5 minutes as it's doing the following; 

• Verifies your startup disk and attempts to repair directory issues, if needed

• Loads only required kernel extensions (prevents 3rd party kernel/extensions from loading)

• Prevents Startup Items and Login Items from opening automatically

• Disables user-installed fonts 

• Deletes font caches, kernel cache, and other system cache files

NOTE 2: if you have a wireless keyboard with rechargeable batteries connect it with its charging cable before booting into Safe Mode. This makes it act as a wired keyboard as will insure a successful boot into Safe Mode.

It shouldn't take that long to just upgrade to a new system. Not unless you're erasing and doing a clean install. I haven't done one of those is 30 years, if at all. Don't remember that far back.

Just be sure to uninstall any "cleaning", "optimizing", "speed-up", anti-virus or VPN apps on your Mac according to the developer;s' instructions and have a full and current backup of your boot drive before starting the upgrade.

I just went thru the same thing after an update to Ventura. Here's how I got all of the rules back:

1 - determined exactly when the update occurred via the  ➙ System Information menu.

2 - created a smart mailbox with all emails since the date of upgrade.

3 - saved all the emails under the File ➙ Save As menu as "Raw Message Source".

4- went into my Home/User/Library/Mail folder and selected the current V folder

5 - entered Time Machine and went back to the day before the system update/upgrade.

6 - selected and restored the V folder that was in the Mail folder.

V10 for Ventura, V9 for Monterey and V8 for Big Sur

7 - when asked selected Replace.

8 - when the replacement was complete opened Mail. Got a message that X number of emails had to be imported which might take a few minutes. Actually it too less than a minute for about 330,000 emails.

9 - double clicked on the Saved As messages and moved them to the correct destination mailbox.

Tom,

I upgraded from Big Sur 11.7.1 to Ventura 13.0.1. I had a custom defined mail header (Return-Path) and one primary mail rule name with about 30 entries [ Return-Path ] [ contains ] [ some miscreant address ]. Upgrading to Ventura disabled the single Mail rule, and removed the custom mail header, and all of the individual [ Return-Path ] rules that I had configured in that main rule name.

I recreated the custom mail header [ Return-Path ] and now as formerly controlled SPAM arrives in my Inbox, I select that single junk message item, and in Mail Preferences > Rules, add back its rule, and then invoking that rule, move the SPAM to Trash.

The only bright side to this is that some of those original 30 rules were no longer necessary and the originators changed their credentials or quit sending crap. Otherwise, it is a manual process to rebuild the rules.

Earlier, I mentioned [ Return-Path ]. Every email sent to you has a mail server authored Return-Path header entry and it is like a fingerprint for the sender. They can change their From email address and domain, but it will still have that Return-Path address. In most cases, these Return-Path addresses are accounts on private, or public Mail servers. When I select a SPAM message and then visit the Rules, when I enter [ Return-Path ] [ Contains ], the text of that Return-Path server is automatically entered adjacent to contains. I then edit that down to just the Return-Path server domain (e.g. spamya.com). When I save the rule, it will whack the selected mail message in real time, and any future emails from that Mail server.

so you are now telling me that I can just reinstall Ventura over the existing install and I'll be done?

Yes.