If the 1099MISC you receive from this company reflects your reimbursements, then you deduct them. If its on the 1099MISC, you essentially received income. You used this income to then pay expenses.
The company is not treating any of these payments to you as reimbursements of valid expenses. It is simply giving you money. It is up to you to itemize the expenses on your tax return.
Alternatively, the company could have set up an accountable plan with you. With this approach, the company deducts the expenses in the appropriate categories on its return, and does not report the reimbursement to you. That puts the expense on their return, not yours.
As long as the reimbursement isn't an awkwardly large amount, I wouldn't worry about the 1099 being a lump sum.
The only possible drawback is meals and entertainment. You are limited to a deduction of 50%, whereas your lump sum may include 100% of it as income. If your employer reimbursed and didn't include in your income, that would be a tax savings.
Rules for Independent Contractors and Clients
