It actually does mark shows as watched and also updates your next episodes.
Firstly make sure you are using the built in player. If you use an external player, it will not update anything in Trakt.
Then sign out of Trakt scrobbling and go to Trakt> sign in,> settings> scroll horizontally across the top menu list,until you find " connected apps" > scroll down until you find " Stremio".
Look to the right and hit the " X" or where it might say " Revoke".
If Stremio is not in the list, it means you have not enabled it in Stremio> trakt scrobbling> authenticate.
But assuming it is in there>>>>>
Go back to Stremio> settings>Trakt scrobbling and authenticate.
Thats you back up and running. And for your information, this is something you may have to do every 3 months or so should you run into issues again.
I am sure that i posted this before on this forum, but cannot locate it.
This issue is well documented on Reddit> sub forum> r/ stremio. I
There is also a new feature that came out a couple of weeks ago, whereby you can now, through the website/ dashboard import all.your Trakt history/ collection for movies and series.
It is pinned at the top of the forum on reddit.
But, if you dont mind paying a few dollars a year, have a look at Weyd and Sinclair.
Trakt updates either app whatever you may have watched on the other one.
Finally, the latest Stremio update of Trakt i mentioned above, now also updates all three of these apps, whichever one you use.