Hello Tom,
If you were using your own SPI code, rather than PE code, you should already be aware when the final byte of the sequence was written to the SPI hardware buffer SPIDR, and when the transmission of this byte actually commenced (SPISR_SPTEF == 1). When the master has then sent all bits of the corressponding dummy byte, SPISR_SPIF will become set, to indicate the completion of the final both-way transfer. Usually the master will raise the /SS signal a short while after this occurs.
If PE function is not capable of detecting the occurrence of this sequence, perhaps you should consider modifying the code generated by PE. You might rename the modified function and/or ISR, to prevent PE from further messing it (and potentially erasing it).
Regards,
Mac