If the initial small claims action related only to property damages, and the second only to pain and suffering then it is likely okay. While plaintiffs are generally not allowed to split a cause of action in superior court, the small claims court will some time allow it. However, it is not appropriate even in small claims to sue for property damage once and then sue again for the same property damage. That would be an easy way to circumvent the dollar limit of the venue.
As the insurer is the one responsible for paying, have their attorneys research this issue for you. It is their nickel, not yours.
Good luck to you.
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The judge was correct on the notion of res judicata. The law here is a little abstract, but basically you can treat injury to your property as one lawsuit, and injury to your body as a second one without running afoul of the rule on res judicata.
If your only issue on appeal is res judicata, then you likely will lose. You may have other issues, however, that are worth appealing. This should be discussed with your claims adjuster, if your insurer is truly on the hook for these claims.