So when running on the newer versions of sar (1.12.4-5) I have issues with portals linking between timelines, I have no issues with this on the older versions of sar (1.12.3) though.
You should try newest SAR version and see if it fixes your problems. https://github.com/p2sr/SourceAutoRecord/releases/tag/1.12.6-pre13
Also make sure you're on the "release" beta branch of the game on Steam. (right click -> Properties -> Betas -> select "release") SAR targets this version of the game, since that's the version we use for runs.
So uhh, after playing around for a bit the issue still seems to be here, is there anything else that could be causing this issue?
FIXED THE ISSUE!! There was a command introduced in sar 1.12.4 pre-8 "sar_fix_reloaded_cheats". All I had to do was set this to 0 and it seems to have fixed my issues.
There are now boards and support for reloaded coop in our speedrunning plugin SAR! All you need to do is update to the latest pre-release (1.13.0pre1) and setup your splits the same way you would a single player run.
Best of luck on runs, and if you have any questions please ask them in our speedr