Recently I see an increasing amount of uppercase one-letter interwiki prefixes, such as [[W:Title]]. Most of them seem to come from VisualEditor edits, e.g. https://www.mediawiki.org/w/index.php?title=Localisation&diff=prev&oldid=1922576
I suspect Parsoid is normalising such wikilinks to uppercase, because most people use lowercase for interwiki prefixes (except sometimes the rare CamelCase ones).
It would be good to get steps to reproduce this, if possible. Not sure what is causing the w:/W: iwp to be used instead of say, :en: as below.
[subbu@earth tests] echo "<a href='http://en.wikipedia.org/wiki/Hampi'>Hampi</a>" | node parse --html2wt --prefix mediawikiwiki [[:en:Hampi|Hampi]]
This happens when you enter a link via the inspector in VisualEditor (ie. you highlight some text, open the link dialog and enter w:Title). Multi-letter prefixes are capitalized as well.
Most of the time such links won't work anyway due to T133535.
Using the steps from T116619#2483981, I get [[w:Title|Testing]]
That seems to be default these days.
I was able to get it to serialize [[W:Testing]] by typing W:Testing, highlighting it, opening the link dialog and hitting return. But that's probably just giving you what you asked for.