Hi,
Can you re-crated the scale set as Virtual Machine Scale Set -> update ResourceGrup/Name/Region/ -> Disk -> Networking -> Scaling -> Management -> Health ->Advanced (Here uncheck "Allocation policy>Enable scaling beyond 100 instances) -> Tag -> Review and Create.
After re-creating by unchecking Enable Scaling beyound 100 instance, you should be able to add back end pool with Basic Load Balancer.
Regards,
Karthik Srinivas