Hi Vasilis,
I suppose you are working with SAP Business One version for SAP HANA (B1H, fully running in top of SAP HANA, no MSSQL server anymore).
There is a tool part of the B1H package that will do the migration of your company databases from MSSQL to HANA. Please check the B1H package -> Documentation -> SystemSetup -> Admin Guide, it is explained there where to find the tool and also how to use it.
Regards,
Trinidad.