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You may refuse to take some or all of your father's estate assets. Typically you would give administrator or executor of the estate a written disclaimer of what you refuse to take. Generally you need to that within nine months of the date your father dies for it to be effective for federal income, estate, and gift taxes. You don't want to miss that deadline because otherwise the IRS will consider you the owner of the assets whether or not you actually take control of them. That's not a tax situation any beneficiary who is going to abandon the property wants to have to deal with.
Bear in mind that what your father owns is the stock of the S-corporation. The corporation has all the assets and liabilities of the business. If you (or the administrator of the estate if you don't want the job) plan to just shut it down then you'd have the corporation sell or dispose of its assets, pay any of it's debts from the asset proceeds, and you'd be done with it. If you plan to sell the business, then it becomes more complex. If the business has more debts than assets, you'd do the same thing, only you want to take care to pay the debts in the proper priority given the applicabe state and federal statutes that would apply. Then after all that is done, the corporation can distribute what's leftover to the estate, which will become the owner of his stock on the day he dies. If the assets exceed the debts then selling either the stock or the assets is probably the best for the estate to do.
Whatever you decide to do, I suggest you run it past a tax attorney or other tax professional familiar with dissolutions of S-corporation and also knows how the federal and state estate/inheritance tax works to make sure your plan won't be too costly.
You are not obligated to pay any of his debts other than those you have personally guaranteed. If you disclaim your inheritance and never become the owner of the stock then the business is not any of your concern unless you are the executor. Even as executor, you would not be liable for the debts of the S corporation unless you give out assets without first paying the estate's creditors.
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