As per the title, toggling the checkboxes on the listIndex Mode documentation tiddler no longer updates the ExampleData tiddler.
listIndex checkboxes do work properly in 5.2.7 wikis.index Mode nor listField Mode has the same problem.(I was a little relieved to find that this seems to be a bug in the release, to be honest… I was initially afraid I’d broken something in my own code with overzealous application of functions. 
)
the listField mode seems to be working, and this is all I used prior to 5.3.0 are you confident it was working earlier?
Yes, extremely. I’d been using it in my own 5.2.7 wiki, which is how I noticed that it was no longer working.
For a live demonstration of what’s supposed to happen, you can also paste the example code (reproduced below for your convenience) into a 5.2.7 wiki, e.g. Shiraz at the current time of writing.
<$set name=indexName filter="[<currentTiddler>addsuffix[ Colors]]" >
<$checkbox tiddler="ExampleData" listIndex=<<indexName>> checked="green" unchecked="red" default="red"> Green or red?</$checkbox><br/>
<$checkbox tiddler="ExampleData" listIndex=<<indexName>> checked="yellow" unchecked="blue" default="blue"> Yellow or blue?</$checkbox><br/>
<$checkbox tiddler="ExampleData" listIndex=<<indexName>> checked="orange" unchecked="purple" default="purple"> Orange or purple?</$checkbox><br/>
Colors list: <$text text={{{ [[ExampleData]getindex<indexName>] }}} />
</$set>
Sorry, I meant to say I did see it occurring., ie I reproduced it
This is a serious matter @jeremyruston or the developers will need to look at.
I’ve created a fix for this bug in Fix checkbox widget when listIndex field undefined by rmunn · Pull Request #7679 · Jermolene/TiddlyWiki5 · GitHub, but it might not make it into the 5.3.1 release as Jeremy Ruston has already annonced a freeze on merging new code into 5.3.1. If the fix doesn’t make it into 5.3.1, the fix will be in 5.3.2 whenever that version comes out.
The fix has been merged into 5.3.1. You can see it working at https://tiddlywiki.com/prerelease/#CheckboxWidget%20(listIndex%20Mode) now, and once 5.3.1 is officially released (quite soon now) you’ll be able to update your wiki to 5.3.1 and have the listIndex work again.
My apologies for causing this bug in TW 5.3.0. I had some quite extensive tests for the checkbox widget, but all of them were written with an existing data tiddler providing the data for the checkbox. So they missed this bug, which only triggers when the data tiddler doesn’t exist or the specific index isn’t found in the tiddler. But it’s fixed now.
Thank you very much for the quick resolution! I hadn’t expected that it would make it into 5.3.1, so that’s especially exciting. 
5.3.1 has been released now, and the listIndex mode is working again, as you can see by using the example in the CheckboxWidget (listIndex mode) documentation. You should now be able to update your 5.3.0 wiki to 5.3.1 and have your checkboxes work.