To replace files (such as .dll's) that are in use, use the "inuse" command at the command-line.
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Note: Before using this command, make a backup of the file you are replacing.
The syntax of the command is:
inuse Replacement Destination
C:> inuse c:TestFile.dll c:windowssystem32TestFile.dll
This command can also be used to grab remote files:
C:> inuse servernameshareTestFile.dll c:windowssystem32TestFile.dll
Use the '/y' switch to suppress the confirmation prompt.
On the next re-boot the file will be replaced.