Hi,
Thank you for reaching out Intel FPGA Community.
If you refer to the Clock Control Block (ALTCLKCTRL) IP Core User Guide, it has mention that when you are using the glitch free switchover feature, the clock you are switching from must be active. If it is not active, the switchover circuit will not be able to transition from the clock you originally selected. Refer link below for the user guide:
https://www.intel.com/content/www/us/en/content-details/654442/clock-control-block-altclkctrl-ip-core-user-guide.html?wapkw=clock%20control%20intel%20fpga%20ip&DocID=654442
Regards,
Aqid