I think we can broadly distinguish two classes of effects here:
- Flares directly affecting the planet
- The by-products of the flare affecting the planet
I can loosely tell you what I know (although my knowledge here is far from being complete)
Direct effects include:
- Magnetic field geometries: Far-away from their host star (>0.05AU) planets usually have isolated dipoles. The solar wind then must penetrate the magnetosphere of a planet to erode its atmosphere. This is however much easier for the wind if due to small distance both star and planet-magnetospheres connect. What this will lead to, is quasi-free flow of a significant portion of the stars total ejected mass towards the planet and huge energy input into the planet's upper atmosphere.
Indirect physics can be:
An active young star can have frequent outbreaks of CMEs, those are accompanied by strong UV / X-ray emission and this will affect the planet:
- Increased photochemistry: This can generate a very active photochemistry in the upper atmospheres. Doubly ionized molecules like $O_2^{++}$ or $N_2^{++}$ can then be produced more efficiently and eject their constituents into space upon dissociation due to high dissociation energies
- UV-X-heating: Additional heat through thermalized high-energy photons can add to the already happening 'natural' atmospheric erosion.
We don't know however, to which extent those effects play a role. I'd add tomorrow some references if you're interested.
There could be signs however of such activity in young stellar systems, as verious combinations or extensions of the above have been proposed to explain the radius anomaly in super-close extrasolar giant planets.
