Has any flying creature evolved into a sea creature?
Clarification of the question
The following feedbacks from the OP are his comments below

By creature of course I denote animals
I meant animals that can fly (not glide) and control their flight
By sea creature I mean those animals that either breathe in water with gills (e.g. fish) or the ones that have to surface to breathe (e.g. whales).

Answer
Water beetles are the perfect example.

They live underwater, some of them very rarely (if ever) surface as they capture air under their abdomen and can breathe it for a long time while underwater. Just like dragonflies, butterflies, flies, bees, ants, bugs and many others, beetles are Pterygota and therefore have flying ancestors.

Answer before clarification
It all depends what you mean by &quot;sea creature&quot; and &quot;flying&quot; as well as by you mean by &quot;semi-aquatic&quot; and &quot;semi-terrestrial&quot; and also what you mean by &quot;creature&quot;.
Here are examples of eventual interest to you.

Birds that are good swimmers, including those that can't fly anymore such as many penguins. No birds can breathe the air dissolved in the water though.

Insects that evolved a larval stage in the water while the ancestors are fully terrestrial. I don't think any insect can breathe under water however several species can carry quite a lot of air with them underwater (such as water beetles) or many just stick their butt out of the water to breathe (like culex mosquito larvae).

It is unclear whether by the use of the term &quot;creature&quot;, but if you accept examples from non-animal forms of life, you'll find examples of seed dispersal through water while ancestors used air, you'll find plenty of examples of parasites too.


If by &quot;creature&quot;, you meant &quot;animal&quot; and by &quot;flying&quot;, you meant high level of control flight and by &quot;sea creature&quot;, you meant animal able to breath air dissolved in the water, then I personally can't think of an example of a flying animal evolving into a sea animal.
None of these examples are as pleasant for you as an example of a big flying bird evolving gills that now live in deep sea though but unfortunately, I can't think of such case.
For fun, you might want to have a look at the post How many times did terrestrial life emerge from the ocean?

Your usage of the term &quot;creatures&quot; as well as the phrase &quot;according to evolution theory&quot; and also the phrase &quot;many sea creatures of the deep past&quot; make it feel like you don't have much knowledge in biodiversity, evolution and evolutionary time scale. You might want to get some intro knowledge on the subject. Understanding Evolution by UC Berkeley is a very introductory and pretty short free online course on evolutionary biology if you are interested in.