Okay, took me awhile to write everything up. The script itself is pretty short, but it's still much easier to do in a script than to try to make this a one line command.

I tested this creating a top level directory, and then creating three subdirectories inside it with a different number of html files inside those directories, and it worked perfectly. I'm going to break down exactly what's going on in the script, but do note the two commented commands. I set this script up so you can test it before actually executing it on your files. In the breakdown of the script I'm going to ignore the testing command as if it were not in the script.

The script:

#! /bin/bash

# script to move all html files from a series of directories into a single directory, and rename them as they are moved by adding a numeric indicator
# to the beginning of the filename, while keeping files of the same folder grouped.

fileList="$(find ~/test -name '*.html' | sort)"

num=1

while IFS= read -r line; do

	pad="$(printf '%03d' $num)"

	#The below echo command will test the script to ensure it works. 
	#The output to the terminal will show the mv command for each file.
	#If the results are what you want, you can comment this line out to disable the command, or delete it entirely.

	echo "mv $line ~/done/"$pad${line##*/}""

	#This commented out mv command will actually move and rename all of the files.
	#When you are certain based on the testing that the script will work as desired
	#uncomment this line to allow the command to run and move & rename the files.

	# mv $line ~/done/"$pad${line##*/}"
	((num++))

done<<<"$fileList"

The breakdown of the script is in the reply comment. Lemmy wouldn't let me post it as one comment.