As discussed a few days ago, I have just committed corrections to the schedule.ccl of various thorns. If you update any of these thorns, then you need to update MoL and several other thorns as well -- otherwise you will have an inconsistent schedule, and time evolution will be gravely inconsistent. (If you fail to update, you are supposed to see an error message.)
In particular, I corrected the schedules of - GRHydro - ML_ADMConstraints - ML_AMDQuantities - ML_BSSN - NaNChecker
and these corrections crucially depend on the thorns - Carpet - (Kranc -- only when you generate code yourself) - MoL - TmunuBase
These schedule corrections ensure consistency during checkpointing and recovery, and correct a few other minor spots. In particular, if you checkpoint and recover, you should now see identical results (except for the pressure, which depends on the con2prim accuracy). Previously, certain operations were missing or were applied twice after recovering, leading e.g. to "weird" constraint values for the next few coarse grid time steps. To my knowledge, the evolution variables themselves were already consistent after recovery up to floating-point round-off (and up to con2prim accuracy).
-erik