Yes you can decide to move to MS SQL Server anytime after the upgrade.
When you upgrade Pulse to v5.6. the first time Pulse starts, it is going to migrate the data from the old databases to the new one, you will see this message on the web client:
After upgrading Pulse, it will use by default the new docs.h2.db database.
So you can continue using this new database or you can decide to use MS SQL Server instead.
You can move to MS SQL Server at anytime after the upgrade, just follow the instruction in the release notes. After adding the MS SQL Server details in the Pulse.cfg, the first time Pulse starts, it is going to migrate the data from the new docs.h2.db database to MS SQL Server.
I hope this is clear,