Noticed some people talk about replacing files folder by folder when applying a new patch. I found a simpler way using the rsync command (which copies files and folders, but it doesn't overwrite folders, it copies the contents of them).
Open Terminal app and run this command:
$ rsync -av ~/Downloads/P99Files52b/ /Applications/Project\ 1999.app/Contents/Resources/drive_c/P99/
* ~/Downloads/P99Files52b/ is the path of the unzipped patch files
* /Applications/Project\ 1999.app/Contents/Resources/drive_c/P99/ is the path to the P99 directory inside Wineskin wrapper app
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