I had similar issues making an on connect light up my room app.
The neo pixel is VERY dependent on timing working. An interrupt on BLE and its callback would likely break the one wire protocol being used by neopixels. There is a new pixel that Adafruit sells that uses two pins, one for a variable clock, and the other for data. Completely independent of a specific clock frequency.
Not idea, however you could save your color data, disconnect, stop advertising, stop ble and then do your color wipe. Once complete ble begin etc. I haven't tested this, but if it is indeed a timing issue and you're getting lost in no ops, perhaps this would resolve that issue?