The one role that the bot does remember if someone leaves and rejoins the server is the Muted role. This is the Muted role the bot creates itself with the Moderator plugin. Not any other role.
If that role is set correctly, as per the embed below, then a member with that role will be Muted and not able to send messages anywhere in the server and will still be muted if they leave the server and then return.
This has been thorourghly tested by MEE6 staff.
I've also seen this in action in my own server and I also saw it recently in the AI server where a member tried to evade a temp mute by leaving and rejoining and then had to wait the remaining time until the tempmute ended.
So if it's not working properly in your server, you need to look again at how you have set it up. And if you continue to have problems with it, #〉refunds for assistance from MEE6 staff.
CC @lunar nymph