Seems to me that you're a bit confused over the proper use of a separatory funnel.
Where in this picture {disclaimer, this is not me, just a picture taken from wikipedia, consider PPE at all times} do you see a filter?
Consider the analogous situation where you have a crude mixture of salt (NaCl) and sand. In this case if you add enough water then it all dissolves. But you can recover some, if not all of the solid by evaporating off the water. If you add less water then predominately the NaCl will dissolve, and you can filter off the sand via Büchner funnel filtration or similar.
In your instance all the organic material has dissolved in your EtOAc, and broken some of the intermolecular bonds so that the resultant conglomerates are smaller than the holes in the filter paper. It's possible that you didn't heat it for long enough, or perhaps too gently (EtOAc only boils at around 78 °C, if I recall correctly) - perhaps try removal of the solvent on a rotovap or similar to recover your solid.
S