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The convert command keeps the data on the partition intact (it worked that way since Windows NT 3.51).
There is one thing you should be aware of:
As soon as you have NTFS on your disk, you have the tighter access control activated. If the computer is used by multiple users, this may lead to unexpected behaviour when you are exchanging files.
Also installing programs under C:\Windows\Program Files\ is typically ony possible as administrator.
In General, I would not recommend the conversion of the windows partition on a system that is already in use for a noticable amount of time. Best do it directly after installation - or even better use NTFS during installation
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