I suggest treating the matters separately.
I assume that you weren't aware of the employee's HIV status until he notified you last week. If true, based on the chronology of events, his condition couldn't have affected your decision to call him in for a meeting for the suspected theft, because you weren't aware of it. However, now that you are aware of it, you should follow EEOC's guidance on engaging in the interactive process for responding when an employee notifies his employer that he is a qualified individual with a disability (QUID) that is covered by the ADA and that disability requires some accommodation. See EEOC's website at http://www.eeoc.gov/ada/adahandbook.html#reasonable. Among other things, you can ask him to submit the necessary medical information to document his medical condition and the accommodation he needs for his condition. You can ask if his current sickness and his treatment will affect his ability to work, how, and an estimate of how long.
You should also consider his FMLA rights if he's eligible for FMLA.
I agree that with regard to the thief issue, you follow your existing procedures. What is your policy for handling potential disciplinary matters when employees are on leave? Do you continue the communication by post or email, or do you suspend it until the employee returns from leave?

