It's been so unpredictable so far, I wouldn't do it until the end. Not that I'm making anything large, anyway, but it seems the more you do it, the weirder things get! I've noticed it also doesn't like anything that's been scaled in the fpe. I have a lot of models from Arteria and I've had to scale some down by half, or double in size. If I've scaled them down, the lightmapper moves them apart. (some dungeon corridor segments that I had linked together. I'm not sure what it does with ones I've scaled up since I haven't run across them yet in my experiments, but I'm sure it won't be pretty! This is just a guess but it may be ignoring the scaling and placing them where their respective origins would be without scaling, but I really don't know.
MAME Cab PC: i7 4770@3.4Ghz (passmark 9945), 12GB RAM, Win 8.1/64, GeForce GTX645 (passmark 1898); Shiny new laptop: i7 4800MQ@2.7Ghz (passmark 8586), 16GB RAM, Win 8.1/64, GeForce GTX870M (passmark 3598); Old laptop: i5@2.3Ghz, 8GB RAM, Win 7/64, Intel 3000 graphics