The Eberspacher Easy Start Pro is compatible with the Eberspacher Hydronic S3 D5E 'CS' model number - 252993.
You are correct, the 'CL' version Hydronic S3 cannot be controller by the Easy Start Pro.
The Easy Start Pro will read the error memory on the heater, give you P000 codes and delete errors, this should remove heater lockout AS long as the fault on the heater has been rectified.
For Eberspacher Hydronic S3 D5E fault codes please see link - Eberspacher Espar Hydronic S3 CL P000 Repair Troubleshooting Manual