How much is an informed answer worth to you?
To properly advise you, an attorney would likely have to review all the documents and correspondence between you and the landlord. A contract generally should be read as a whole instead of in bits and pieces.
Hiring professional help is an ordinary and often necessary part of running a business. If you do not now have a business relationship with an attorney, you likely should look into finding one or more attorneys who can advise you on various aspects of running your business.
I don't know what you mean by the "comments section". I will assume that this refers to part of the lease containing substantive terms, not just informative comments. The new manager's interpetation is almost certainly wrong. I haven't seen the entire lease document or any correspondence, so I'll have to put it this way: If the lease says that the comments section terms are not part of the renewal terms, then the new manager is right. If the lease says nothing about the terms in the comments section being inapplicable to the renewal term, then those terms are applicable to the renewal term.
But that doesn't mean you can win an argument. Your best move might be to simply tell her that you believe the entire lease has been renewed, that you will be paying the agreed rent on time, and then drop the conversation. If the manager tries to evict you using the proper legal processes, you should win. If the manager evicts you without using the proper legal processes, or interferes with your business to force you to leave, sue for breach of contract.
One more thing. Since you are leasing a part time office, others have access to the office. You should have copies of all important documents made and kept at home. You should make daily backup copies of all computer files and take the backups home. You should have a hidden camera covering your office so that if some thief steals your computer and your files, you will know who to sue.
This answer must not be relied on as legal advice for the reasons posted here: http://mcgyverdisclaimer.blogspot.com . And I am not your attorney.
As I read your post, I am reminded of how so many commercial tenants don't have their leases reviewed by an attorney before they sign them. A lease review and evaluation can be done in an hour or two. The best couple hundred dollars you will ever spend. One of my colleagues has a number of frugal tenant clients. They have learned never to sign without a quick review.
Conversely, in your situation, an attorney experienced in commercial leases, could probably review an evaluate your situation in an hour. People will spend great amounts of money on clothes, but they won't spend a few dollars on a contract that has huge financial implications that last for 5 or 10 years. My point is obvious. Spend a few bucks to determine your situation. Nobody can truly evaluate your situation without looking over the documents.