After searching for hours, I finally found what I needed. I found this information online in an Adobe manual called "Creating Accessible PDF Documents with Adobe Acrobat 7.0." I have Acrobat XI, but the instructions still transferred over from 7.0 to XI easily. I'm going to paste them here for others to reference:
Creating Tags for Links That You Made Active Late in the Workflow
To be accessible, each link a PDF document must have three tags, presented in the following order, in the tag tree: a parent <Link> tag, a child <Link - OBJR> tag, and a child document content tag. The <Link> tag alerts a screen reader to the presence of the link. The <Link - OBJR> tag enables screen readers to present the link. The document content tag identifies the content on the page that comprises the link.
When you use the Links tool or the Create Form URLs In Document command on a tagged PDF document, Acrobat tags each URL by adding a document content tag to the tag tree, but it does not also add a <Link> tag nor a <Link - OBJR> tag. A link that does not have a <Link - OBJR> tag is considered an unmarked link and is inaccessible to assistive technology. You must locate all instances of unmarked links in the tag tree, and then add <Link> and <Link - OBJR> tags to them, by following the instructions below:
To find an unmarked link and add <Link> and <Link - OBJR> tags to it:
1. In the Tags tab, choose Options > Highlight Content, and then choose Options > Find.
2. In the Find Element dialog box, select Unmarked Links from the Find drop-down menu.
3. Click Find. The first unmarked link is highlighted on the page.
4. Close the Find dialog box. Use the select tool to select text that is near the link, then choose Options > Find Tag From Selection.
5. In the Tags tab, select the document content tag for the link (the tag that names the URL), and then choose Options > New Tag.
6. In the New Tag dialog box, select Link as the tag type and click OK. A <Link> tag appears below the selected document control tag. Drag the document content tag down to be the child of the <Link> tag.
7. Select the <Link> tag, choose Options > Find, and then select Unmarked Links fromt he Find drop-down menu.
8. Click Find. Acrobat finds the URL that you have been working with.
9. In the Find Element dialog box, click Tag Element. The following two things happen:
- A <Link - OBJR> tag appears as a child to the <Link> tag directly above the document content tag. The tagging for this link is complete.
- Acrobat highlights the next unmarked link in the document.
10. As needed, repeat steps 4 through 9 on the rest of the unmarked links in the document.
Below is a sample image from my PDF.
I had added hyperlinks to items in a Table of Contents late in my accessibility process ("3 Overview...." in the example below). I then received the Tagged Annotations - Failed error. Following the above steps, I:
1. Clicked the "3 Overview..." document content tag.
2. Created a new <Link> tag.
3. Dragged the "3 Overview..." document content tag under the <Link> tag to be its child.
4. Clicked the <Link> tag (always make sure you do this so it places the <Link - OBJR> tag in the correct spot).
5. Used the steps to find unmarked links.
6. Clicked Tag Element. This added the Link - OBJR tag in the correct spot.
After that, I ran my accessibility check again, and the Tagged Annotations - Failed error was gone! I hope this helps others as much as it helped me!