Hi,
I'll try to address as many as possible of your specific questions.
When you import the HSK words from Mike's list in the first post of this thread, you can configure the import to merge duplicate cards with pre-existing cards. That will mean that any card you had added to the flashcards database before the HSK import will not be duplicated but instead belong to both the HSK and your previous categories (that is the same card).
Once that is done, when you wish to study cards that are
both in the newly imported HSK categories and in your pre-existing categories, you can find just those cards and add them to a new, empty category afterwards.
You can first create a new category named "My HSK Vocabulary", or similar. In the magnifying-glass search feature in Organize Flashcards, choose Search for
category and select the HSK category, then add the second search criterion, Search for
category and select the category where all of your pre-existing cards are stored (Perhaps you will first need to move all of your pre-existing cards inside a single category folder.). The two search criteria have to be linked together with AND. The resulting list of flashcards can then be copied to the empty category named "My HSK Vocabulary" by selecting them all and choosing Set Cat and the empty category. Then the relevant cards will belong not only to the HSK and your pre-existing categories, but also to the new category; they will be in at least three categories.
As I see it, you would need to repeat this process every couple of months. You'd select all cards in "My HSK Vocabulary", remove them from the category (not delete them), then repeat the above process. No records of your studying progress are lost, since the cards are still there, just not in the "My HSK Vocabulary" category.
-Is there any way to get this square border to reflect only the the flashcards/words that are NOT in the HSK categories?
Not directly, but you could configure a tag for the HSK categories and a tag for your "Encountered words" category. (in the info screen for a category in Organize Flashcards) Then at least when you open the full definition screen for a word, you could tell by the tags in the upper right corner whether a word is just in HSK or you actually encountered it/wish to study it.
-Do I just delete the entire HSK list of flashcards EXCEPT for those words that already existed prior to the HSK import (presumably the HSK categories and tags would remain)? How would I do this?
The Search feature in Pleco 3.2 doesn't allow you to add a NOT search criterion (unlike the Card filters in Flashcards). At first blush I wouldn't recommend it, anyway, because then you couldn't know if any future cards you add to your pool of cards-to-learn are also HSK vocabulary. You can still only study cards that are in both categories by using the combined category from above.
Hope this helps,
Shun