As long as both were changed to f4i tubes it _might_ be okay. I looked at replacement tubes from tnk, and found the lengths of the tubes are indeed different. F4i is 587mm, and 919 is 615mm. Bushing placement may further impact how far they can extend.
They other concern I would have with a shorter tube is having the damper rod bottom out on the compression valve. Maybe check with the shop to ensure they check the forks through their full travel to ensure there is no interference.
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'96 DR650, '01 SV650, '10 Aprilia Tuono 1000R