KNOWN ISSUE: Running aexagentutil.exe /clean on client machine uninstalls agent AND Windows system32 files

Cause
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Please note that this is NOT a regression in ITMS 7.5 - the problem was also applicable to earlier releases and happens only with custom changes for log file path location. 

In this particular instance, the customer had the incorrect SMA agent log file path in the registry (check “FilePath”under HKEY_LOCAL_MACHINE\SOFTWARE\Altiris\Altiris Agent\Event Logging\LogFile). Removal process uses the entries "FileName" and "FilePath" from "HKEY_LOCAL_MACHINE\SOFTWARE\Altiris\Altiris Agent\Event Logging\LogFile"
Another option when this could happen is when there is no logging folder specified in the registry, in this case uninstall will try removing files from the process's current folder, which can be anything in the general case.

Solution
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Symantec has acknowledged that the above-mentioned issue is present in the current version of the product mentioned earlier on this article. Symantec is committed to product quality and satisfied customers.

Symantec currently addressed this issue by including a fix in the ITMS 7.5 Hotfix 2. See DOC7076

Development changed the Agent behavior where it should not remove all the files from this folder, only agent*.log files, then it should remove the folder only if it’s empty. Currently agent tries removing the complete file tree.