This old bug has resurfaced now that people are playing the switch version. https://reddit.com/r/invisibleinc/comments/he281u/dlc_characters_not_working_on_switch_version/
I figured out a way to reproduce it. Start or load a game that has the DLC disabled. Then, without restarting the game, start a game with DLC enabled. Any items added by the DLC will disappear, can be verified if you start with one of the new agents. Log will look something like this:
[LUA] Missing upgrade 'augment_ambient_turbine' when applying to unitData id=nil, name=Olivia
[LUA] Missing upgrade 'item_crybaby' when applying to unitData id=nil, name=Olivia
[LUA] Missing upgrade 'augment_particle_envelope' when applying to unitData id=nil, name=Derek
[LUA] Missing upgrade 'item_transport_beacon' when applying to unitData id=nil, name=Derek
This happens because the table in upgradedefs only updates once, the first time createUnitData is called. The table needs to be reset after every time mods are loaded.
The mod Sim Constructor already fixes this issue so if you're using that you don't have to worry about this.