@obo: honestly, what i started doing is saving before every combat. if things don't go well for you, reload. it takes longer, but it guarantees that when you make progress, you get to keep it.
BTW, I have a solution for the "cat and mouse" issue that happens when trying to find a battle. the main issue is that as your fleet gets bigger, it gets slower and it becomes harder to catch anyone. so here is my solution.
I propose a major change of the way the travel overlay works. instead of having 1 fleet that you control directly, I would like to see a much more RTS like approach, where you can have multiple fleets, and you control them like units in an RTS. thats how you control your single fleet now actually, so all I am asking is to be able to have multiple fleets that can be controlled as one or separately. also something to make the control system a bit clearer, such as waypoints when you select a destination.
When you enter into a battle, all of your owned ships would be available to call in, not just the ships in the fleet you used to initiate the combat. This would make the concept of your other ships being "reinforcements" make more sense, because they are ships from another fleet coming in to help.
In addition to fixing the cat and mouse issue, this will lay groundwork for much more complex gameplay strategies, allowing you to have your ships in different places doing different things at the same time. for example, you can have your mining and transport craft in one fleet, running a supply line between a base and a meteor belt, and you can have another fleet patrolling that supply line, while you have a 3, small and fast strike group hunting down pirates (which is how it solves the original issue btw)
In fact, I even foresee a slight variation of the command point system translated to the travel overlay, so you can assign tasks for various fleets, or create waypoints on the map to rally specific fleet types, build space stations, along with plateforms to defend them, etc.
bottom line, this will allow you to scale much more effectively.
BTW if this is what you have been planning on doing anyway, awesome