A few things come to mind: Is it really full sun where they are growing? I found with a number of baptisias I planted that they did fine until some got shaded when nearby shrubs and taller perennials grew and cast too much shade. Baptisias will sometimes take time to settle for a year or so after transplanting, so that’s another possibility (though I haven’t had them totally fail to flower for two years, personally). Another possibility is that when cleaning up the bed, someone stepped on the area where they were not yet emerging, but about to. If you have ever seen baptisia stems when they first emerge, the flowers-to-be are already there, right at the tip but not expanded yet. They are easily crushed in early spring by a badly placed footstep. Mark your plants carefully to prevent this next year. Any of that register as a possible answer?