Not much info to go on here.

Soft particles do a compare against the depth value which controls a fade-to-transparent as they get close to intersecting.

If your transparent meshes were to write to the depth buffer that the soft particles are comparing against, then it'd probably work. Note that the depth buffer the transparent meshes need to write to may or may not be your main scene z-buffer. It may be part of a G-buffer or something.

Can you provide more information as to what exactly isn't working correctly with your transparent meshes?

@MJP: Since the transparent meshes are not writing to the Z buffer, the particles are not soft when intersecting with transparent mesh.

So then have them write to the z buffer.