Good ideas above, but it may not work all the time, depending on what you have after the filters in processing-chain in the synths, sometimes it can end up dull rather than giving a nice lowpass effect for example (I'm especially thinking of a pluck sound consisting of several layers as an example).
Since you mention automation CLIPPING, I assume you work in FL, since that's the only DAW that uses the term "automation clips" and not just "automation" to my experience (correct me if I'm wrong).
If you do use FL, one thing you could is using the "link to controller"-function. Rather than automating all filter in all synthlayers, simply automate 1 filter on 1 synth, and then you rightclick on other just as you normally would, but instead you click on the Link To Controller, and a box shows up. In the box you see the section "Internal Controller", click where it says "(none)" and select in the list that pops up the name of the automation clip you want to link it to, then click accept, and bam, your automation clip now controls several knobs at once. This is pretty handy, but I bet it can be a bit unhandy if you deal with different types of synths whose filter respond differently.
Buuut if you dont use FL and I'm wrong, just ignore this.