To perform skew checking for elements before and after the BUFGMUX, you can apply a FROM:TO constraint. If the elements before the BUFGMUX are grouped in TIMEGRP A, and the elements after are grouped in TIMEGRP B, the syntax is as follows:
TIMESPEC TS01 = FROM A TO B 12ns;
Another option is to have related PERIOD constraints for TIMEGRP A and TIMEGRP B. If these two PERIOD constraints are related to each other, then the clock skew will be analyzed correctly.
For more information, see (Xilinx Answer 7221).