The home office deduction is allowed or not allowed on its own facts, regardless of whether your office is "Registered" according to some state law.
For a W-2 worker, you must meet three tests to deduct a home office. The space must be used exclusively for work (not also used for personal living space), it must be your regular place of work, and it must be used at the convenience or direction of your employer, and not merely for your own convenience.
Assuming those facts, then you can deduct your home office expenses, but only if you pay them yourself out of pocket or after tax. If your employer reimburses you and the expenses are included in your W-2 box 1 income, then you can deduct the costs as an itemized deduction limited by the 2% rule using form 2016 and schedule A. However, if the employer is paying your costs and not including them in your taxable wages, then you can't also take a tax deduction. That's double-dipping; if the money is already tax free, you can't deduct it again.
You don't say, but I'm guessing the employer paid your costs tax-free, and that's why they registered your home as an office, so they could do that. That's probably why you were audited and you probably lost the deduction. If I guessed wrong and you want more information, post a comment or reply with more details.
