I had just recently downloaded starforge. I opened a map that I had been making with Xtra 2.5, and it turned all the gates I had places in one direction, and when I saved it and played it, the trees and other doodads where cut off.
I know how you feel, it happened to me. There is no current solution unless you replace all doodads that have been affected. Or use SCMDraft.
Just use SCMDraft on completion of the map, and it will revert these "sprites" back into "doodad" format.
Thanks Coko you are a big help.