As of recent Riot/web versions old messages that can't be decrypted in rooms will not be shown (saves the user from being blasted with Unable to Decrypt errors).
So the messages are likely there, but you won't see them until you import your e2e keys.
Jitsi is much easier to add in the latest Riot-web version. No longer do you need to set up your own integration manager. You just add the jitsi URL to Riot's config.json and you're done.
How long ago did you try Riot? It's changed a lot in the past year, and with their encryption changes coming in the next few weeks it should be even nicer.
I use it to set which site I'd like to keep cookies for multiple sessions for, and which I'd like cookies to be forgotten for as soon as I've left. It doesn't have per-cookie granularity however, if that's what you're looking for.
Ideally you'd be using multiple workspaces, and only have 1-4 windows on a single given one.
I like to organize my workspaces by a category of activity. I'll have one per project I'm currently working on, then one for communications (Email, Chat, etc) one for web-browsing, etc.
I try to keep the non-project ones consistent, so at any point I can, say, tap Meta-9 and instantly be brought a web browser on Workspace 9.
So the messages are likely there, but you won't see them until you import your e2e keys.