This is not a StackOverflow question, this belongs to ServerFault (admin). It toucehs dev though-
i.e. deleting a record from the table is like execute delete command, but doing this I'll not result in physical
deletion of file from NTFS...so how can I delete a file physically
Do you know what the primary reason is to hav a database? Guarantee data integrity.
A delete must keep the data around until a backup is taken. What is your backup policy? YOU may note that when you make an update, another copy of the file is created.... for that simple reason. The old one must still b e available for backup, and that is just how they integrate it.
In which format file is stored at FilestreamGroup1 (for every single uploaded file I found 2 encoded file)?
No, files are stored raw. What would be the sense to encode them... if there are SQL functions to get the path and it is a supported scenario that the client does not use SQL to load the file (but: asks SQL for the file name and path, then accesses it via NTFS file share). This also supports interop (as any program loading from a network can be fed a SQL driven location.
I strongly assume you have 1 copy only and somehow make an update resulting in a second file written.
http://msdn.microsoft.com/en-us/library/cc645962.aspx
has an explanation how to access FileSTream data with SQL.
http://technet.microsoft.com/en-us/library/cc645940(v=sql.105).aspx
has an explanation how to access FIleStream data using Win32.
FILESTREAM files being left behind after row deleted
explains while files are left behind when a row is deleted. I found that using the extremely trivial goodle search for "sql filestream delete file" and it was item 1 on the result list - did you even try google?