They usually don't stick their heads out unless they are after some food. My ex-boyfriend had one and he would disappear for weeks. Then eventually we would worry and dig around in the gravel and he would reappear. Try enticing him with food. Maybe that will make him come out of hiding.
About the filter, you could try getting a piece of foam and attaching it to the intake with a rubber band. I have never tried it, but it was mentioned to me when my HOB was bothering my betta.
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*Kristin*
5 Planted tanks:
55g, 40g, 29g, 10g, 5.5g
10g N. multifasciatus tank, 5.5g Platy fry
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