No, you do not need to preserve the unused transmitter pins of an E-Tile Channel PLL on the Intel® Stratix® 10 or the Intel Agilex® 7 E-Tile FPGAs.
Example: If your current design implements an E-Tile Channel PLL in location 4 that clocks E-Tile channels 0-3 in External EMIB Clocking mode, you do not need to preserve the TX pins of channel 4 if that channel were later to be used as a data channel instead of a Channel PLL.
This information will be added to a future revision of the E-Tile Transceiver PHY User Guide.