Hi, we have a fix for the rule issue prepared for the next update (not the current 10.0.3447 unfortunately) but there is a workaround that can resolve the bug without an update (or need to re-make all rules).
Go to Menu>Accounts
Open the POP or IMAP tab of the affected account.
Change any detail in this tab - for example the number of days the messages should be kept on the server or the sync options etc. (You can change this back later of course)
Save this change.
Restart eM Client.
Now the rules should be applied correctly and you can reverse any settings change you made previously.