Hello, and welcome to the forum.
Since TCLK is a lower priority, alternate pin function to TPM1CH0, it would be intuitive that TCLK should follow the the repositioning of the channel pin - is this what you have observed?
However, this would seem to be at odds with the datasheet, in Table 2.1. Here, TCLK is shown to be associated with PTA0 only, as an Alt 3 priority. What functionality have you observed for the PTA0 pin, after PTC0 becomes the TPM1C0 channel pin?
Perhaps you should generate a Service Request directly with Freescale, to have the matter clarified. If the datasheet does contain an error or ambiguity, this can be corrected for a future release of the document.
Regards,
Mac