You are correct, unique upgrades are designed to alter the game play style of the ship to offer a new play experience. For example, take a look at these two examples:
All of them increase some factors, but reduce others.
You have 2-3 months to complete your current grind progress on your current upgrades. Currently, if you do not complete it by this time, you will lose your amounted progress, however we may have more details on this later.
Speaking of details:
Progress on specific missions wont be saved in a sense that you won't be able to complete them - they will be deprecated. But some sort of compensation for achieved progress will be there, (esp if you were really close to receiving one), the exact volume/procedure is still being discussed, and we will share the details as soon as they are finalized.
Fem,