Yes you are eligible for isolation pay and yes you will be paid! She took the shifts off because she either had to reassign them to someone else or erase them completely so the SSV doesn’t get confused and try to call you in. She can put in your isolation pay before deleting them and you’ll still get paid. I hope you feel better!

She doesnt get to “delete your shifts”. And doing shady shit like that is a very quick way of getting fired. I however, suspect your manager removed them from the partnerhours to assign them to someone else and not maliciously. I also have no idea how isolation pay works now as the company has made it extremely confusing based on vaccination status etc. Would check in with your manager politely about the missing shifts.