If SMP/E is asking for the use of the BYPASS(APPLYCHECK) parameter on the ACCEPT it is because the FMID has not been applied. It needs to be applied before it can be accepted.
The IBM documentation explains the use of BYPASS(APPLYCHECK):
Indicates that SYSMODs should be accepted even if they have not been applied. For example, if you are preparing the distribution libraries before doing a system generation, you want to accept SYSMODs that have not been applied.
Note: APPLYCHECK can also be specified as APPCHK.