Flex Time doesn't alter the original Audio File. WIth the help of the Transition Markers and Flex Markers, you only define sections in the waveform that gets time compressed or time expanded (plus pitch shifted). Basically you are only manipulating (shifting) existing data in a non-destructive way.
To actually mess around and delete specific data (notes) inside the waveform, you have to use Melodyne. What you can do with this plugin to an Audio FIle is close to magic.Hope that helpsEdgar Rothermich
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Just FYI, you can turn flex off for particular regions on a flex enabled track by looking in the inspector: top section at the bottom is a check-box. This is useful if you only actually need flex in a few places, and also for troubleshooting - if you enable flexview and set the track flex style, but are not getting results, make sure the box is checked.