You don't clean it you replace it with a new one

Your local Honda dealer should have the oil filter bolt. You should also have a spring and a washer in there to hold the filter in place. The new filter should come with gaskets for the bolt and the cup. Ask the service dept how to put it all together. The cup should have two tabs that straddle a tab on the engine to keep the filter from spinning, be sure to get it on correctly, or it will leak.
Did you look in the container you drained the oil into? Maybe it fell in there.

What oil filter?
The centrifugal one,,behind the round cover on the R/H engine cover?

The "missing bolt" is a 6mm hole ,,recessed in the center of the cap?

That's a PULLER BOLT Hole.
The Cap gets stuck very badly sometimes,,,and that hole accomodates a 6mm bolt to be screwed into it,,,which presses against end of crankshaft to Push the cap outa the "filter" cup.

The puller hole normally has Nothing in it,,,leave it as an open hole.

Be VERY Carefull dealing with that filter.
Once the accumulated sediments are disturbed in Any way whatsoever---even from just removing the cap---,,,if Not 100% Thoroughly cleaned the crud can come adrift and become resuspended in the oil circulation.

That may sound implausible,,,,,"why wouldn't any particulates simply be centrifuged out of suspension again,,as usual?"

The thing to realize is that a "pin head sized" clump of that sludge represent the accumulation of DOZENS of Hours of Run Time.

So even very,very small pieces are an extraordinary Concentration of particulates.

When in it's native state lining the centrifuge walls,,,it's near impermeable by the oil.

Any time it's disturbed,,it once again becomes "Soluable" in the oil.
Especially in modern oil's detergent packages that wanna suspend "anything".

The APPEARANCE is deceptive.
You can Clean it and have it LOOK "clean"...while theres actually a Thick cake of crud remaining.

Make CERTAIN You have all that stuff ABSOLUTELY Clean.
Including the Cap and it's O-Ring,and the Retaining ring.

Otherwise,disturbing it simply creates a metallic slurry that's pumped Directly to the connecting rod bearings,,,and that's Not a happy meeting.
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That's the Only "Missing Bolt" I know of in those things.
It Does look odd,though.