Aperture understands the raw files as generated by the camera. If you make changes/tweaks to them in 3rd party software (like Sony's) it's likely the raw files aren't interpretable by Aperture.
The only way I know to fix it is to use the originals; perhaps there is a way in IDC to reset all adjustments on the photos.
TIFF would be the better call. "Truly lossless" is difficult to say; changes are "baked in" to the RAW file on the conversion.
Still, the PTlens plugin recommended in another thread is probably the better call: