Atlas is apparently using BLMA's tooling, so those same models will probably see the light of day again. Atlas has already announced a new run of the NS Top Gons in N scale using BLMA tooling. Considering that BLMA did make an excellently detailed line of models I doubt that Atlas will just let that expensive tooling go to waste after purchasing it. Whether they'll continue with BLMA's line of detail parts and so forth is a different question entirely.
I have a tendency to believe that BLMA or at least products from their tooling will live on. I think that Atlas bought BLMA for the name recognition that they had earned as a very high quality product. There is too much value in the BLMA name to just let it fall by the wayside.