Nonissue! Changing gauges can throw off your setup, but it has to be a pretty wide swing. Going from 10s to 9s or 11s only adds or subtracts a few pounds of tension; the effect on neck relief would be the same as changing your tuning (minimal if not flat out negligible).
Try some different products and gauges, you might be surprised at what you like.
I tried flatwounds for the hell of it and found I really like them, especially on my Jets. I generally go with Thomastik-Infeld Steel/Nickel Flat Wound Extra Light, .010 - .044, but they're a bit pricey.
For roundwounds, I like RotoSound Nickel Electrics Yellows .010 - .046, and they're reasonably priced.