The lease mentioning them putting up the stuff as security doesn't mean your father's LLC has a perfected security interest such that the landlord is even free to hold stuff hostage if the tenant wants to claim it didn't leave it behind but that your father/the LLC changed locks/whatever. That's what the attorney was likely referring to.
"Tenant hereby agrees to execute and deliver financing statements from time to time at Landlord's request for the purpose of perfecting and serving notice to third parties of the security interest herein granted."
Ah, but evidently the landlord didn't pursue refusal to do so as a breach.
As already mentioned, it's not at all clear that the property in question was actually owned by the tenant (and there may not be much in the way of accounts receivable to go after even had the security interest been perfected). If not, failing to ascertain that (and making sure tenant agreed not to put the stuff up as collateral for any loan in future) before bothering to lease the place to them was a mistake.
It's also not clear whether your father ever gave them proper default/breach notice under the lease, but I presume so. And did your father/the LLC get a personal guaranty from individuals who were members/owners of this tenant LLC? I hope so, if the company fell on hard times.
"My step-dad's lawyer is now telling us the contents of the building belong to the lessor and we have no recourse to sell this property to secure the past-due amount they owe."
Read this again; it's garbled. Your father is the "lessor" in the scenario you paint, so ... please clarify. You also do not identify who you mean by "we".
"But the lawyer said something about filing the value of the contents with the county and to be honest, I didn't quite understand what he was saying and he didn't seem like he wanted to put it in laymans terms for me."
You don't say who you are in this equation, but the lawyer's almost certainly talking about the landlord LLC not having perfected its security interest in the stated personal property/equipment/inventory.
"Now one thing I know the Tenant's never did was deliver financing statements even when we requested them."
And your father/the LLC did ... what in response? What's the consequence in the lease provisions for refusing to do so and did the landlord declare a breach?
"So do we have any options?"
That's not a question reasonably put to strangers, I'm afraid. Obviously, the landlord is free to sue the tenant for breach of the lease. Twelve grand isn't a ton of money, so I wouldn't spend a ton of money on an attorney to pursue even if the lease calls for the tenant to cover attorney fees in the event of breach.