File not found at path when trying to copy

Try with File::copy($file, $dest) instead of Storage::copy($old, $new)
File::copy() is the wrapper on PHP's copy() function

You said that the error is like this:

File not found at path: var/www/apk.land/storage/extracted_apks/res/drawable-xxxhdpi-v4/icon.png

Here error is saying it cannot find at var/www that means it's looking for apk.land/var/www whereas your file is located somewhere at /var/www. A quick fix to this can be use file protocol. Just use it like:

file:///var/www/storage/apk.land/storage/extracted_apks/res/drawable-xxxhdpi-v4/icon.png