Does flounder now mean founder?

The simple answer is that some people make the mistake of confusing the two terms - but that doesn't mean the mistake has become "standard English". There is a clear semantic difference between the two words. The following definitions, from Merriam-Webster, demonstrate the difference in meaning:

flounder
intransitive verb

1. to struggle to move or obtain footing : thrash about wildly
   The poor horse was floundering in the mud.
2. to proceed or act clumsily or ineffectually
   the normally surefooted governor floundered a moment like a prize pupil caught unprepared –– Time

versus

founder
intransitive verb

1. to become disabled
   especially: to go lame
2. to give way : COLLAPSE
3. to become submerged : SINK
4. to come to grief : FAIL

Oxford Living Dictionaries provides a further clarity:

founder 3
[NO OBJECT]

1. (of a ship) fill with water and sink.
   ‘six drowned when the yacht foundered off the Florida coast’

   1.1 (of a plan or undertaking) fail or break down, typically as a result of a particular problem or setback.
   ‘the talks foundered on the issue of reform’

Here's my own summary of how the two words might apply to a given situation:

Sometimes something (e.g. a project) will indeed both flounder (struggle, or be ineffective) and founder (collapse or fail). However, there's a sequence here: a project can't first founder and then at a later point flounder. As an analogy, you can't die and then get sick.

Note also that something that flounders may not ending up foundering, and something that founders may not first have floundered. To use the mortality analogy again, you can die without getting sick, and you can get sick without then dying.