There are only two instances that the canister can travel safely:
1) When unlocking Gonarch's Lair via a portal.
2) When placing the canister on a teleporter to send it to a secret area in Gonarch's Lair.

In case of the first one, the canister also must be in your hands as you jump into the portal. Throwing the canister in the portal will not work. As for the second one, you need to set the canister down on the teleporter machine and then activate the teleporter controls.

Doing anything else with the canister other than these two things may result in the canister not being able to go with you or being lost forcing you to restart from the Xen Labs the canister is found in (if you don't have earlier saves and have to use chapter select).

Originally posted by Engamer01:

There are only two instances that the canister can travel safely:
1) When unlocking Gonarch's Lair via a portal.
2) When placing the canister on a teleporter to send it to a secret area in Gonarch's Lair.

In case of the first one, the canister also must be in your hands as you jump into the portal. Throwing the canister in the portal will not work. As for the second one, you need to set the canister down on the teleporter machine and then activate the teleporter controls.

Doing anything else with the canister other than these two things may result in the canister not being able to go with you or being lost forcing you to restart from the Xen Labs the canister is found in (if you don't have earlier saves and have to use chapter select).

I'm talking about the teleports in the chapter Xen.