Can I reconfigure application to use FQDNs of servers instead of IPs?

Assuming 1. the iApp does not support FQDN 2. you are running a version of BIP-IP that supports FQDN based nodes

Then you can disable strict updates on the iApp (on the properties page of the iAPP). You could then create the new nodes manually and replace the pool members. However, any subsequent updates to the iAPP would overwrite your changes and you would need to perform the same changes again.

If you are running a version of BIG-IP that does not support FQDN nodes (11.6 I believe is the first release to do so), then even manually making the changes with strict updates will not truly be using FQDN. Prior releases allowed you to use an FQDN, but only during the creation process, when it resolves it to an IP and uses the address instead.