you can create a band subset based on the entire stack and un-check all faulty dates. This will ensure correct handling of metadata.
I am not aware of such an option which allows to define an initial shift for individual images.
@SimoneA How large (in pixels) is the offset? The automated estimation of initial offsets offers windows of up to 2048 pixels width.
One last thing to try: Apply the orbit file and then range-doppler terrain correction using “complex output” and “nearest neighbor” resampling of the data. If the data is projected correctly, you can use the terrain corrected products as input for the coregistration and select “Product Geolocation” instead of “Orbit” as Initial Offset Method. Maybe this tricks SNAP into correctly overlaying the input data, although there might be new issues because the data are no longer in slant geometry. But worth a try.