When you link for example Calendar 1 with Calendar 2, you will have one FreeBusy account with a unified availability from Calendar 1 + Calendar 2. Any link you share will display your unified availability (ex. the event template link from Calendar 1 or the event template link from Calendar 2 will display a unified availability from both calendars).
If you choose to separate Calendar 2, you will have 2 FreeBusy accounts, one for Calendar 1 and one for Calendar 2, with 2 separate availability links, one availability for Calendar 1 and one availability for Calendar 2. People booking a meeting with you using a link associated with Calendar 1 won't see your busy times from Calendar 2 and vice versa.
If you choose to remove Calendar 2, you will delete your account associated with Calendar 2 and all your available links for Calendar 2.