The minimum clock frequency on IFCLK is 5 MHz, so one can't shut it down. The reason being , the logic needs to be alive enough to keep up communications with the SIE to know when to update packet pointers.
First of all make sure that external IFCLK is free-running. There cannot be any stoppages in the clock. The external IFCLK source must be present before the SX2 configures the IFCONFIG register to set the part in synchronous mode. The SX2 comes up with the internal IFCLK source selected, so power-on configuration is not an issue.
However, typically, the IFCLK will be generated from an external master. The external master must guarantee that IFCLK comes on before the SX2 IFCONFIG register write occurs to set the part in synchronous mode using external input to IFCLK. This will keep things in sync.
So yes, one can change the IFCONFIG register in from async to sync (with a driven IFCLK).