My proposal is the following:
In the Yes-winning scenario, the remaining UK should be constituted of England, Wales and Northern Ireland. While the current flag represents the order of the kingdoms joining the Union, the design in the hypothetical could represent all the constituent countries in same way. The yellow cross on black background represents Wales, the red saltire on red stands for Northern Ireland, while the red cross overall represents the England. If Cornwall eventually become a constituent country, part of yellow fimbriation can be turned white. The saltire is completely red, and not counterchanged red and white like in current flag.
At least two other questions about vexillology can be resultant of the hypothetical scenario: the case of the ensigns and the royal standard.
Ensigns: They don't need to be changed. For this occur, it only needs that, while the national flag is changed, the current naval jack is kept. The now-independent countries that still adopt a British ensign (Australia, New Zealand, Fiji, Tuvalu, Cook Islands) can also keep it for historical purposes.
Royal standard: It could be an excellent opportunity to Wales be represented in UK royal standard. However, its inclusion can be ambiguous, as the Prince of Wales uses the "royal" coat of arms of Wales (as used in Wales and in England and Northern Ireland). Other options are quartering England and Northern Ireland, or marshalling them, for example.
As it's a very complex issue, I invite you to leave your opinion on the comments.
This post is about vexillology, not politics. Comment gently, please.