I actually found a suitable solution elsewhere at InDesignSecrets, buried in a comment from Daniel Rodney in response to this post:
https://creativepro.com/convert-numbering-to-text-in-indesign.php

First, I tried 12 different solutions to get KindleGen to work. Nothing would work. Amazon KDP forum and Amazon Support could not solve it. I was tempted to manually convert all numbered lists to text manually by typing 1 2 3 before the text, but I did not have the patience to do this thousands of times.

But then I found Daniel Rodney’s shortcut. This shortcut ruins your file, so Save the original file with a name like MyBookBeforeNumbersRemoved.indd. Then, Save As the file as MyBookNumbersToText.

Say that you are managing numbers with three paragraph styles:
NL
NL-RestartAt1
FigureNumbers

Select any paragraph that is NL (those are the ones that go 2, 3, 4…)
Open the Paragraph Styles pane. In the top right corner is a menu with an item called Convert NL Numbers to Text. Select this.
Repeat for NL-RestartAt1
Repeat for FigureNumbers

I took the time to add a Tab (^t) to each paragraph style, in the Bullets & Numbering:
Figure ^#^t

I also added a left-tab at the 1 inch mark in the Tab well (also in the Paragraph Styles)

I was able to convert thousands of numbers to text in about 5 minutes.

Then, export as ePub3.
Convert the ePub3 to Mobi using KindleGen.

Success! All of the numbers move down to the same line as the text.

I had a similar problem. Here is where I found the problem:

My INDB file included six INDD files.

I had to open each individual INDD file and go to the Cross-References panel. Sort by the status icon. I had a “Red flag with white X” icon. The cross reference was pointing from Section1.INDD to Section2Recovered.INDD. At some point, the Section2Recovered.indd had been renamed to simply Section2.indd.

Here is how to fix:
1. Click the cross reference in the Cross References panel.
2. Use the Panel menu and choose Relink Cross Reference.
3. Point the cross reference to File2.INDD and the problem went away. In my case, they were pointing to Section2Recovered.indd, which at some point I renamed to Section2.indd. It was easy enough to see that the old cross reference was pointing to Section2 and to find the current version of Section2.
4. Repeat for any other missing cross references in this file. Repeat for each additional INDD file in your INDB.

Also helpful: Sometimes, re-linking one cross reference would automatically correct others. But I had to fix each relationship once. For example, fixing the link to Section2.indd from Section1.indd did not help similar links in Section3.indd or Section4.indd