I assume what you mean is your business paid for the improvements, and deducted at least a portion of them through expensing or depreciation.
What should have happened is you as landlord should have reported the improvements as rent income while you deducted the expenses through the business. Then, you could have added the improvements to the basis of the building and deducted them off the sale proceeds.
The improvements are an allowable deduction, but it seems they weren't reported properly. At this point in time, you may be able to argue that since you own both entities that you should be allowed to add the undepreciated improvements to the basis of the property, but that may not stand up to an audit.
If you don't add the improvements to the basis, which is the safe thing to do at this point, you would not have to factor any depreciation recapture on them either, since they weren't added to the basis.
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