I make a point of keeping an unit of friendly cavalry hanging near them for those occasions. I've noticed even the most close-order heavy cavalry can move through sufficiently loose-order friendlies (Hunters on standard and most other archers on loose, for example) almost like they weren't there, which in practical terms means countercharging right through the archers to give the enemy cav something better to do.
And that's only on the flanks of or away from the main infantry line. If you're skirmishing your archers back and forth through the main line, I've found it best to just plain keep an eye on the enemy cav and manually tell the archers to take a hike early enough if need be - if you don't, then even when all goes well the speed of the horses tends to be great enough in relation to that of the archers and their "skirmish trigger" range that if you're lucky the cavalry crashes into their rear around the same time they overlap and mess up the infantry line, so some micromanaging is recommended.
Personally, unless the enemy is about 100% infantry or otherwise rather slow-moving I tend to stick my archers behind the heavies. Just plain safer that way. And the AI is tactically inept enough that I still tend to beat it in firefights, assuming equal range or better range.
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