Actual: https://incubator.wikimedia.org/wiki/Wy/zh/Special:Search/foo
Expected: https://incubator.wikimedia.org/wiki/Special:Search/foo_prefix:Wy/zh/

Since the Chinese Wikivoyage has been created, an alternative example would be:

http://aa.wikivoyage.org/wiki/Special:Search/Foo -> http://incubator.wikimedia.org/Wy/aa/Special:Search/Foo

Ideally, the link should point to http://incubator.wikimedia.org/wiki/Special:Search/Foo_prefix:Wy/aa/.

As a side note, this issue also affects other special pages, templates and categories that are treated differently in the MediaWiki context. The redirecting script should be modified accordingly in mediawiki-config (under missing.php in wmf-config) so that these exceptions can be handled.

This is probably better handled on the WikimediaIncubator side than the missing.php side - what the correct prefix is depends on a lot of wiki-specific config that isn't really available in the context of missing.php - ideally https://incubator.wikimedia.org/wiki/Wy/aa/Special:Search/Foo should redirect to http://incubator.wikimedia.org/wiki/Special:Search/Foo_prefix:Wy/aa/

(and ditto for https://incubator.wikimedia.org/wiki/Wy/aa/Template:Foo, https://incubator.wikimedia.org/wiki/Wy/aa/Module:Foo, https://incubator.wikimedia.org/wiki/Wy/aa/Category:Foo, etc.)