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.:
evselect table=mos2S003.fits:EVENTS
withfilteredset=yes
expression="(PATTERN=12)
&>I(mosaic_mos2S003-gti.fits,TIME)
&&((FLAG & 0x766aa000) == 0)"
filteredset=mos2S003-clean.fits
filtertype=expression
keepfilteroutput=yes updateexposure=yes
filterexposure=yes
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.