From memory, fleeing from battles only works when you're miles away from the enemy ship, preferably next to a ship-combat map edge. But the further from the enemy the better. If you're faster then them you're fine('ish), if you're not then you get caught('ish).
Ingame, this means that if you're fast and agile you can just retreat (possibly with another battle shortly afterwards, but try and retreat better next time), or if you're slower you can fight. You can just pick either top or bottom of the map as a full-speed-ahead-to-the-other-side-of-the-map-captain! option and blow right past them, even if you're slower, just hope you pick correctly and then retreat as you hit the other side of the battle area. I'm not even sure if ship-combat-maps have edges now, but the further you are from your enemy and the faster you are, the better. Yes, all those ship upgrades are worth every credit.
Meh. I'm going to have to do those hours of gameplay I said I would. Too much information from too many versions ago. I could just say "Get two disintergrators/disruptors (whatever) and you'll be fine", but ship combat had an over-haul.
Actually, that's why I like ProspectorRL. It's complicated, it's a voyage of discovery, but it's not terribly well wiki'd. So I probably know a lot more than some, but heaps less than other players, but I'm not really sure if my experiences are atypical or not. I could look at the source code, but meh. I'll "finish" the game one day. Today maybe