whiteout or .wh files are created in pupsave file of a frugal install when
-builtin packages are deleted using remove_builtin
-a file from a loaded sfs (pupxxx.sfs, zdrv or other) is deleted
-a pet is uninstalled
Their purpose is to mask files which can't actually be deleted so they disappear from directories, menus etc. For example, if files 1 and 2 are present in pupxxx.sfs and file2 is "removed", the result in the layered file system is:

what you see    file1
pup_ro#file1    file2

.wh.file2 and file2 disappear after remastering.
The files from an uninstalled pet and the associated .wh files disappear when the system is rebooted.

Layered file system
Help screen of remove_builtin

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