Problems with Administrative tools after system restore

I have customer server that was recently infected with Ransomeware.  Long story short I had a tech that was restoring the files and folders but instead restored the C and D drives corrupting the server so that I had to do a bare metal restore.

I have everything working again and data restored before the infection happened but now when I look at my Administrative Tools I see two entries for each one from the Server Manager .  One normal as you would expect and the other with a .lnk~ with a random number after it.  I looked in System32 and see two of each but these have DLL~ random number on the second one.

I'm not seeing much information on the web about this so I was hoping someone could let me know if I can delete these or if I have a bigger issue.

The server is a Windows 2012 Essentials server.

Thanks
blkfootAsked:
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William FulksSystems Analyst & WebmasterCommented:
Sounds like user profile corruption. Can you login with a different account that has admin credentials and see if it does the same thing?
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Roshan Gerard BolonnaSoftware Engineer, R & DCommented:
Some viruses harder to remove using Anti-Virus software tools, you might need to scan using special Malware removal tools like "Malwarebytes"

step 1:
Perform thorough scan and remove any  infection using Malwarebytes

step 2:
Then restart and perform System File Check  using "SFC" command as mentioned below

Run CMD (As administrator)

then type following command:

sfc /scannow

this will restore system files automatically while scanning and verifying windows system files.

after completing restart and check if the problem still exists.
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Shaun VermaakTechnical Specialist/DeveloperCommented:
Post both of those files to VirusTotal
https://www.virustotal.com/
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blkfootAuthor Commented:
Thanks for the responses.

William - when I log on with a different user that is an admin the duplicate files are still there.

Roshan - I already ran Malwarebytes and it didn't find anything.  I have to wait until tonight to run the system file checker.

Shaun - I ran a few of those files through VirusTotal and they all came back clean.
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Shaun VermaakTechnical Specialist/DeveloperCommented:
William - when I log on with a different user that is an admin the duplicate files are still there.
Of course, it is. It is in SYSTEM32

Shaun - I ran a few of those files through VirusTotal and they all came back clean.
Missed that the one is LNK. Just delete LNK file
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blkfootAuthor Commented:
Thanks, Shaun.  I also ran the SFC and it came back fine.  I am just going to delete those files.
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