Unless the different pointings have strongly different mean count-rates, it is best to run the soft proton filtering on the multi-pointing ODF. The GTI file created in that process for a given instrument can then be applied to the individual poiintings for that instrument, e.g.:
&&((FLAG & 0x766aa000) == 0)"
N'est-ce pas? If there is a significant number of pointings, then executing this for each instrument of each pointing would become onerous, but that can be relieved by relatively simple scripting.