We have updated the product stock alert module to the latest version 1.2.9 as you suggested but the stock alert emails are not working in the production.
After investigating I have found there was an issue with the function “retrieveAffectedData” that split the collection into a batch size of 2000 records but every time collection returns only the first 2000 records when it goes in a loop.
There is a bug in the Out of Stock Notification module: If there are more records than the batch size (the default module set is 2000, which means there are more than 2000 subscribers), then the module only sends stock alert emails to the first 2000 people and stops.
To temporarily resolve the issue, please download the file StockEmailProcessor.php attached below to override the current file on your site.
If you need any further assistance, please feel free to contact us. We'd be happy to support you!