I have found an issue when using converted saves. I first noticed it with my oldest save I wanted to carry on from. The issue is most of the ship weapons will not work (such as the Laser Cannon and EM Turent). The combat will treat it as through it doesn't have enough energy (despite having more than enough).
I tested it by creating a new save file in Backer 0.9.008 (download) and creating a fresh save in 0.8.159.
The fresh Java file had no issues with the Laser Cannon firing but the one from Flash didn't work. I later tested to see if it was all weapons by adding Machine Gun with the Laser Cannon and only the Cannon didn't work.
I tested it by creating a new save file in Backer 0.9.008 (download) and creating a fresh save in 0.8.159.
The fresh Java file had no issues with the Laser Cannon firing but the one from Flash didn't work. I later tested to see if it was all weapons by adding Machine Gun with the Laser Cannon and only the Cannon didn't work.