We had our current windows here in SC done with 3M film. We have low-e and double panes. And yes, the film will void the warranty with any company.
But 3M does offer a service that you actually buy a window warranty from them, which they cover for the same time as the original warranty. It is relatively cheap and for peace of mind we purchased it. Basically what happens is that if a window cracks due to stress, 3M will replace the window as well as the film up to the original mfg warranty period.
Can't say for other companies what they might do, but this is what we have with the 3M film.
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