Changing your plan/minutes will not affect your upgrade eligibility. I would be willing to bet that it is just because your request is still pending. It's probably something to do with your account being "active" or "changing" and you just have to wait for that to clear.
Now, the only thing I could think that would be a problem, is if you changed your entire plan. Some smartphones aren't compatible with some older plans. In that case you would just have to call Customer Service and have them change it for you, no big deal.
When you "downgraded" your plan minutes online, the change was scheduled to go into effect on the first day of your next billing cycle - hence the change is still "pending". Post dating the plan change will avoid any pro-rating fees and makes the billing much easier to understand.
As Vereyezuhn said, this did not affect your upgrade date, but trying to process online shows the pending plan change. The online interface does not allow more than one change at a time, so you are unable to process the upgrade until the plan change takes effect.
Customer can likely resolve this for you and get you the same online deals. Given them a call.