After creating a new country in Alliance, I realized I was unable to upload my stats to the two website my alliance uses. At some point, both had become unchecked. I promptly re-checked them, but the ominous message stating "THIS WILL NOT AFFECT EXISTING COUNTRIES!" seems to indicate that I will have no auto-uploading of anything this set. Is there anything that would have caused my preferences to be changed without my knowledge? Is there any way to get my changed preferences to take effect on my current country?

Additionally, one trouble-shooting technique I was advised to try was to reset my API Key. That option is not available to me. I looked for it in both Chrome and IE and even after clearing my cache and everything, the option was still not there. I even confirmed where it was supposed to be in chat, and its really not there.

I'm hoping all my issues are merely user error, because that is (usually) an easy fix. Please tell me where I am wrong.

portal preferences give perma check (country prefs only for current country(/countries if ffa)) and changing settings should affect existing countries.

You have to go to the main country preferences. The system is a bit confusing and needs to be redone a bit, it's a consequence of independent development =/ it's on the list

There are 2 places you can change your preferences:

From the portal page: Affects all new countries, the countries copy the settings you set here on creation.

From your country page: Only affects that country.

I'll check it out when I log in to my country - hopefully it will be an easy fix by checking out the in game options page and changing it there. I still don't understand though how this worked seamlessly last set and doesn't work now, even though I literally changed no options.

Also, should I be able to refresh my API Key in the Portal level options page, or is that handled in the individual country options?

not sure; might be individual

Inside your country, scroll to the bottom of the main menu. Click preferences. Here, you can set up the sites for auto-uploading as well as changing your API Key. If you click the Options link in the top left corner of the screen - WHETHER YOU ARE IN YOUR COUNTRY OR NOT - it will go to a completely different and unrelated set of preferences that happens to include many redundant features. The Site Auto-Upload options at this location do not automatically take effect and you cannot refresh your API Key here either.

Hooray for User Error! I still don't know how my "Portal Page Preferences" (which I consider a misnomer since the link says "Options" and persists even while inside my countries :-) changed, but it is a moot point as I now have the power to fix the issue myself. This thread may now be closed.

I considered it "Portal Page Preferences", since it can be accessed from the Portal Page, and to highlight the point that it is not linked to any country, though you CAN access it from within a country.

What it does and how it functions is not how it is labelled. Had the people troubleshooting the issue with me been more deliberate with their terminology, this thread might not have been necessary.

To be fair though, most of the wording and phrases and even menu layouts are copied from Mehul's game, to give it a look and feel that is identical to the original game.