Hi jondon.
The problem is, that all the Faces of a Mesh are numbered:

When using a Subdivision Surface Modifier:

When you now Apply the Subdivision Surface Modifier, all the Faces get re-numbered:

So, if you have carefully placed one hair at each side of the Cube, they are now clumped together at ‘one’ side.
Something similar happens to you; in Sculpt Mode your topology must somehow be different and therefor the numbering has changed. (Maybe through Subsurf or Multires or Dynamic Topology…)
You can also make a separate strip, Shrimkwrapped to the eyebrow (/eyelashes) area and use that as a Particle (Hair) Emitter.