The sceneries "PhotoHD" by FranceVFR are quite "simple" sceneries which just a big set of BGL files. There are no dlls like OrbX sceneries for example.
As a consequence, they do not need any kind of conversion for P3Dv4 compatibility. You can simply declare them into your scenery library and you're good to go
The autogen by Vogel and Jpp is in the same situation: just a big set of .AGN files that you should drop into the "texture" folder of the photoscenery (that you might need to create, since photosceneries will probably have only a "scenery" folder but no "texture"...).
There is no problems linked to 32/64 bits with these.
The trees by Oscar are a bit more special case. They use some kind of alpha blending which works only in P3D, and doesn't work in FSX for example (trees would display well, but they would not be transparent).
I don't know if they work in P3Dv1 or P3Dv2, but they were made specifically for P3Dv3 and they work beautifully in P3Dv4

And yes, they are supposed to impact all of the trees (or almost all) in the sim, not just on FranceVFR sceneries.
I strongly suggest you to make a backup of the P3D\Scenery\Global\Texture folder.
FranceVFR has updated their AGX package just a few weeks ago to make it compatible with P3Dv4. As this package also installs some trees textures (if I'm not mistaken), the Oscar trees should always be installed after, not before AGX.... and maybe the same logic applies to OrbX sceneries.
EDIT: in case you have some additional PhotoHD sceneries, the Vogel and Jpp have also produced the same freeware autogen for the "Rhone Alpes" and "PACA" regions