Flash being phased out? / PDF portfolios

In the near-term, yes.  If you asked me what things look like in 2027 or 2037, I have no idea.

There *are* people on Acrobat that are focused on long-term archival issues, and it's an important topic.  It's *way* outside of my area of expertise, and I didn't realize that it was even a thing that people worked on until it came up in passing the other day.

If your organization has an enterprise support agreement with Adobe, this is a great conversation to have with your support rep to see if they might have some advice tailored to your specific situation. 

If not, you might want to strike up a conversation on the Acrobat message boards around best practices for long-term archival and compatibility, to see if they have any advice.  One option might be to add a post-processing step where you break out very simplistic versions of the final documents for long-term archival at the point that the documents are no longer actively worked on (and this might imply adding the right metadata to ensure efficient discovery, etc), but continue to leverage the robust features for productivity and ease of use while those documents are actively in use.

We don't have visibility into what changes are going to happen over the span of the next few decades, but if you have serious long-term archival needs on those timescales, it would definitely serve you well to have a concrete set of plans and standards for your organization, and a pragmatic approach that prefers simplicity on that front will probably serve you well over the long-term.