Downsampling requires an anti-aliasing filter if you have recorded frequencies which are out of the Nyquist critera for the rate of destination. For example going from 96khz to 44khz you need an anti-aliasing filter if your recording system, for example your microphone, is able to record frequencies bigger than 20khz which is not the case most of the time. These high frequencies cause artefacts when downsampling if they are present. But as you can see most of the time they should not be there or coming from other noise sources. By first applying a low pass filter to reduce the bandwith should allow you to eliminate this high frequencies and then you should be able to downsample your record normally.
But here, we are talking about programs using impulses in 44 or 96khz and impulses are not audio files. I will be surprised that downsampling an IR will be the same thing then downsampling an audio file.