In WW2 it was common to guard key bridges in the rear of an advance needed for the supply lines of the spearheads with flak units.
Perhaps just an addition of flak units capable of destroying/damaging the small engineer helo units with their AA factor will deter such a tactic. Make the AA units have a fire ability instead of movement factors so they are thus "fixed" to bridge guard duty. That way the flak can not be used for additional gamey moves. They will not add to the number of units at the front disrupting your current play balance. If necessary, make several batteries part of an at start S/O so the enemy player with the engineer helos will not know exactly where they are placed. There does not need to be enough flak to guard every bridge, but enough so this tactic can not cause serious harm unless some risks are run by the helo engineers.
If the AA units are strong enough to put the engineers "on foot" those guys should be good as dead. Being flying engineers should make them an expensive VP unit, so using them in such a flippant way would cost the owning player their capability and some hefty casualty VP.
As to the forest hide and seek tactic, if I had to hunt helos with ground units, I would use some mobile flak units in the "hunting party". With a little thought it would be like hunting quail or pheasant. Pull!
Just some thoughts.
Dog Soldier
Fast is fine, but accuracy is everything.
- Wyatt Earp