After applying a wim archive captured with --source-list, I experienced some broken NTFS permissions problems. Here is a test.
Create a simple directory structure :
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md D:\test\abc
md D:\test\xyz
echo > D:\test\abc\sample1.txt
echo > D:\test\xyz\sample2.txt
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wimcapture.cmd list.txt archive.wim --source-list
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D:\test\abc /abc
D:\test\xyz /xyz
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rd /s /q D:\test
wimapply.cmd archive.wim D:\test
Recreating the folder with the command md D:\test before the wimapply operation does not have any effect, the same problem appears. Applying the same archive to the root of a partition is dangerous as all the NTFS permissions of the partition are removed :
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wimapply.cmd archive.wim R:\