Everybody has their own opinion about this but this is the system I use. You do it on the radio so you get real time results. After the proper filter is applied to just your system you then go to sentinel making the target the SDS 100 and transfer the card data to the computer and this will save the changes that you made.
You go to Global filters, Global filters affect every object in the radio and should only be used to sample filters. You don't want to try auto filter as that will slow scanning way down and you already know what normal does. You are going to try the global filter of invert, wide invert and wide normal while you are observing RSSI level, noise level and error rate. Some claim RSSI is not a good indicator but I use it anyway. Just listen for a while and see what helps the skipped transmission. When you find out of those 3, the best filter then return global filter to Normal as that will apply to every object that you haven't gone into Site options or in the case of conventional frequencies Department options and changed. You want global to stay normal because you don't want to compromise any objects that work well on normal.
Drill down on the menu to site options of the system you want to change, apply the filter to your site that you found works best out of the 3 you sampled.
Back out of menu and now you will have that filter just applied to the site that you listen to on your one system you're having a problem with. If you're going to experiment with filters on different objects you might want to add the filter indicator to your display to help keep track. Don't forget to go right to sentinel and transfer the card information To your Profile after you target the SDS 100.