So I'm tryint to migrate my savefile to 2.0, everything is fine except this error:

The mod Project Cybersyn (2.0.5) caused a non-recoverable error.
Please report this error to the mod author.

Error while running event cybersyn::on_train_changed_state (ID 26)
Unknown item name: deadlock-stack-coke
stack traceback:
[C]: in function 'newindex'
__cybersyn/scripts/factorio-api.lua:693: in function 'set_combinator_output'
cybersyn/scripts/train-events.lua:18: in function 'set_comb1'
cybersyn/scripts/train-events.lua:223: in function 'on_train_arrives_station'
cybersyn/scripts/train-events.lua:470: in function <cybersyn/scripts/train-events.lua:413>

While I do understand there will be problems dealing with old/unsupported mods, I think crashing the game is a bit excessive.

As a workaround you could load your map in Factorio 1.1.x, disable central planning in the Cybersyn map settings and let deliveries settle down. That should make sure there are no in-flight deliveries with unfulfillable manifests when upgrading to 2.0. Factorio can also be downgraded via a Steam "Beta" channel.