An internal link inside flow, that points to an interwiki (that is, not on the wiki itself but another that can be referenced using internal link syntax with the corresponding prefix), it's not encoded at all.
Example:
[[w:en:Wikipedia:FAQ#How do I change my username/delete my account?]]
Points to:
https://en.wikipedia.org/wiki/Wikipedia:FAQ#How do I change my username/delete my account?
But it should point to:
https://en.wikipedia.org/wiki/Wikipedia:FAQ#How_do_I_change_my_username.2Fdelete_my_account.3F
If the link points to the local wiki, the anchor is encoded properly. See Topic:Tesyta6rspc1pysm for a test.
Note also that the link is rendered as class="external" instead of class="extiw" as it would otherwise on normal wiki pages. Normal wiki pages render this correctly.
Another interesting case:
[[w:Wikipedia:Sandbox?action=edit]]
Points to
https://en.wikipedia.org/wiki/Wikipedia:Sandbox?action=edit
But when editing the message, the edit text is now:
[w:Wikipedia:Sandbox?action=edit w:Wikipedia:Sandbox?action=edit]