If the CLA is using the ePWM or ADC Result registers, does it mean the main CPU can not?
No. Both the CLA and the main CPU can access the registers. The arbitration scheme for these registers can be found in the CLA Reference Guide. Keep in mind if the main CPU performs a read-modify-write operation on a register and between the read and the write the CLA modifies the same register, the changes made by the CLA can be lost. In general it is best to not have both processors writing to registers.
