Unfortunately, Clear Transformations will not reset the image to 100% size in all cases.

But, once you have the image selected (NOT the frame, but the image), in the bar at the top of your screen you can find a field that shows the scaling percentage of your image. It is the right-most field shown here (the fields that show 87.301813 in my example):

Make sure that the little lock to the right of these fields is selected, and then change the value in either of those fields to 100%.

Now your image has been resized to 100%. You can confirm by checking the Scale: field in the links panel. If there is nothing shown in that field, then the image is not scaled at all--meaning it is at 100% scale.

Depending on your document and workflow, you may now need to resize the image frame to fit the image, or adjust your image placement within the frame to show the portion of the image you want to show.

You will have to perform this transformation individually for each image (or there may be a script out there that will let you do them all at one time), but once you have made the transformation to the first image, you can use Object > Transform Again.