A reference to a Typedef-ed control should know which Typedef it is associated with. I mentioned a slight lack of feature regarding this one year ago.
It is very likely that if you have created such a reference, you will use it to access your control's value in a subVI, like this:
If you take a look at such a subVI, the reference control can look two different ways.
Like this:
or like that:
if you have chosen to "Show Control" rather than "Show Icon".
The control in the reference box above "knows" that it is associated with a Typedef, and you can access that Type Definition from the reference control in its second form above (but not in its first form, which is a variant of the problem I mentioned in the thread cited above).
Now, if you modify the definition of the Typedef itself, here is what happens on your diagram (after having used "Apply Change" on your Typedef):
The wire is broken, even though both objects know that they are associated with the same Typedef.
The magic "Ctrl-Run Arrow" will fix that, but there seems to be no reason why the wire connecting a reference to a typedef control and a similar control in a subVI should break.
I'd say this is a bug.
Note: This might be vaguely related to this older report of mine here.