Yes, you can.
Let me give you a brief explanation how scheduled synchronization works: a bitmap driver starts tracking all changed clusters on the disk before the cloning starts. When the time for sync comes, a VSS snapshot is being done on the source volumes, and all the changed clusters are read from that snapshot and transferred.
You can also instruct Converter to stop some services before the final sync, e.g, SQL server and exchange. Thus there will be no lost data from those services' activity.
HTH
Plamen