For the side mission Generous Donations, there is text under The Virus that states "At the end of each round, heroes claim 1 neutral mission token for each terminal on the map. Then, increase threat by the threat level." Does this mean:

A. It's an end of round effect, so in essence the imperial player will increase threat twice during the status phase (1. Increase Threat, 2. Ready, 3. Deploy and Reinforce, 4. End of Round Effects - give tokens to rebel players and increase threat", 5. Advance Round Dial)

B. It's just stating that rebel players get tokens before the imperial player raises threat at the beginning of the status phase.

I lean towards A because they specifically mention increasing threat as opposed to just saying that rebel players get tokens at the end of round. I can't seem to find the answer anywhere.

I would suggest it is B.

end of round - give rebels the tokens earnt - increase threat - ready - reinforce - end of round effects (e.g. moving the laser of death from ord mantell royal guard mission)

I'd say it's A!

First of all it includes the special wording "end of round". And also it fits thematically that the more the rebels can upload, the faster the imperial reinforce.

It's definitively A.

As stated in the rules : Step 4: End of round effects: If there are any abilities or mission rules triggered at the end of this game round, players resolve them at that time.

So it will happen after the deployment step, thus, yes its a second increase in threat, but not one you can use to reinforce during that round.