If the signal went through the filter, and if the filter is missing, then you would need to bypass it by joining the pins that the filter connects (as a quick fix while you don't have a replacement filter), but, if the filter is connected to the signal and then to ground (like it seems from the picture), then you don't need to bypass anything, because the signal will reach its destination regardless of the filter presence.
Anyways, if the missing filters are on unused ports then you don't need to replace o bypass them since they are unused, nothing bad will happen.