Basically the launcher systems used are all the same in both JP and US versions, except for the destination where the patch files are to be read.
For some reason the launcher might have read the cache from the JP version, leading the launcher to download patches from the JP server.
When this happens, as the launcher automatically deletes files which are incorrect or corrupted, it will start deleting all the files from the JP because they are different from the US version.
Until an official fix is announced, what you can do is to try deleting all caches from your IE or browsers.
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