You are right. Unlike in HW1, here you can't collect resources and manage production and research of your fleet after all battles are over and objectives met. You have to think about this during intensive battles. And another thing new in HW2. Large ships, like capital class ships leave some nice amounts of RU's after you destroy them. Auto-collecting-resources-at-the-end-of-the-mission will not cover those RUs left from destroyed ships (thanks Alrik for pointing me to those excellent forums, where I have got this info).
So, it is essential to :
- first, collect all parts of destroyed ships,
- second, think about what fleet will you have at the beginning of the next mission.
DAD, to be precise, I will have to replay at least previous mission to gather resources and strong army. Hmm, there is sense after all, maybe this is the best thing to do, as I enter this mission broken and weak.
