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After you use the "speed" option (like slowmotion) on a clip, you cannot crop it anymore.
Because the speed option makes your clip longer or shorter its not possible afterwards to line it up with music or whatever...
I think you mean Split (to cut out unwanted frames). Cropping zooms in to cut out visual areas in all frames, and that works even when the speed effect is applied.
You're right that the clip cannot be split to adjust its duration once a speed effect is applied, so you would have to estimate the new length (or measure it precisely) then remove the speed effect and estimate (or calculate precisely) how much to trim/split from the original clip so that your clip plays for the desired duration when the speed effect is applied again.
Another option may be to adjust the speed effect directly until the duration matches your other timeline content, since that shows the timeline position as you move the speed slider.