Well to be honest I've found the sprite/animation editor functionality in Construct to be pretty bad, you're much better off handling sprites in 3rd party programs and then importing them. But you're already stuck so here's the best thing I think you can do:
First of all, make sure your file is saved as a .caproj, not a .capx. This way your project is multi-file and by navigating to your project file you can find your images in its Animations folder. Back it up to somewhere else on your hard drive. All your image files are in nested folders first under the name of your sprite and then under the name of the animation.
Now inside construct rclick in the "Animation frames" window and use "Import frames" to import the correct frames from your back up folder into the correct animation. You can select multiple files at once to speed things up a little. Now delete all undesirable frames/animations from within construct and continue this process until you're done.
Note that you *have* to do importing, frame addition/deletion, and animation addition/deletion within Construct. Construct doesn't react to filesystem changes unless you're replacing an image your project is already using.