That is not a Yealink flaw and can be changed.
When you make changes to Yealink config files and update the phone from EPM, Yealink phones reboot because FreePBX sends a SIP notify message to the phone that forces a reboot:
If you don't want the phone to reboot, put this in sip_notify_custom.conf
The phone will still reboot with changes that require a reboot to be applied, such as VPN, or other network settings. But most changes will get applied without rebooting, which is much more convenient.
This also works: