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$Secure:$SDS:$DATA File in Partitions?

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So I had a problem with my Windows drive not booting to login screen recently and managed to solve it. The first thing I did was checking all drives for errors and corrupted data, and I found out about one particular file, the $Secure:$SDS:$DATA. The problem is I did defrag jobs on a regular basis and I've never seen that data before, even in any of my 2-3 years old drives. It's something related to NTFS metadata, although I don't know the purpose. But now almost all partitions in my drives plugged to my system have it. Some partitions have over 1 or 2 MB in size, some others about 200-300 KB.

Me and my friend, we ran some tools to check the drives after fixing my boot files problem, and there were some tools with "Partition" as a part of the name (I couldn't recall the names). We used Macrium Reflect too. I'm guessing one of those tools is responsible in creating that file in my partitions. The problem is after searching about it, I found some posts from other people claiming the file will get bigger over time, with some people claiming they have the $Secure:$SDS:$DATA file as big as 3-5 GB. They also claimed they couldn't remove or shrink it, with the file kept growing and eating up their free space. I found out that some defrag tools like Defraggler cannot detect the files, but O&O Defrag can. And some people claimed they couldn't even defrag the file like they could do other system files.

I did an experiment to remove the file by formatting (quick format) one of my partitions that had the file. After several chkdsk, sfc, dism and defrag jobs, I didn't find the $Secure:$SDS:$DATA file in that partition anymore, meaning my current OS (Windows 8.1 Pro 64-bit) or anything installed in my OS didn't create it. Obviously, otherwise I would've noticed the file in my partitions 1-2 years ago considering I always did defrag jobs on a regular basis.

The question is since I can permanently remove the file and it doesn't come back after formatting the partition and removing it doesn't affect the partition in any way, is it possible to remove the file with some commands or tools? Other than formatting every single drives and partitions of course.

I don't know why I've got the file but I'm telling you I'm not comfortable letting this file sitting on my partitions, especially in the drives I'm using for backups. I read from other people's claims that this file will grow bigger over time. Remember that I've never had this file for years until me and my friend running some drive/partition tools, and after formatting the aforementioned partition, nothing I did could create or restore the file (it's gone for good). It has something to do with NTFS metadata, but all my drives are GPT (except for my Windows 7 drive, which is MBR) and all partitions including those of my Windows 7 drive are NTFS and like I said, I've never had this file for years in any of my partitions.
 
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Can't say I have ever seen that file from my experiences, but it sounds suspicious.
 
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If you weren't sharing data, or if you haven't moved data from other accounts on other systems the file shouldn't exist unless some application is using multiple aliases to access data
 
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