I expect it would have a bad impact on the intonation, as the bore of the head would be generally larger than the maker intended. Remembering that the small contraction of 19 down to 17mm tapered over the length of a Boehm flute head is the equivalent of our entire body taper in conical bore flutes. So an increase from say 19mm to 19.6mm over 60mm or so would tend to flatten the upper octaves. (Interesting little modelling challenge there, Tunborough!) And you'd need to make your stopper cork bigger too!
So I'd do the gluing, clamping and making good, and then ream the head out to accept the full length of slide. Now, I know that some households don't run to a full set of flute reamers, hard to believe isn't it, so you could opt to sand out the bore, using a piece of dowel in your pistol drill, slotted to take a course strip of sand paper. No pistol drill? OK, this is going to take a bit longer....
You'd need to proceed carefully, as it would be easy to make some sections of bore larger than you need, although that would not be a tragedy. When you have the slide capable of being inserted and removed without risk to the glued crack, you are ready to glue it in. A few things to keep in mind: - you really want to make sure to line up the embouchure holes in slide and wood, or you'll then have to file the metal through the hole, - you only really need to glue around the hole to make sure it's airtight. That also makes it easier if the crack reopens in the future. - you definitely need to avoid getting any glue down where the female slide from the barrel has to enter its cavity - wise to use a glue that could be softened with heat if something goes wrong, now or later. It will need some gap filling properties.
Best of luck! And make haste slowly!
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