@raspora I just ran into this myself. (Well maybe different, but will share anyways to help others) Applying the Bevel Modifier with seemingly nothing happening at the object level.
Transforms and Scale for me were applied and I also ran the M to see if I had stray verts. IN the end I had missed Jonathan unchecking “clamp overlap”. Once I did this and set my Amount to .01 cm I was back in the game.
