Hi cestcreative
We cannot know what happened on your site. You have seen that CleanTalk has flagged some files as "potential malware", and if it removed any file from ATUM, that could break your site, indeed. As it would happen if it removes files from WooCommerce or from WordPress or from any other plugin...
We can assure you that there is no malware at all in ATUM code, and that was, for sure, a false positive.
ATUM is actually stable and has no known issues that could cause a crash in the latest version.
If you want to know what is really causing that on your site, with so little info. I would recommend you enable the error logs (if you don't have them enabled yet) and check the logs. If it was enabled when it happened, probably, it was registered there.
You can learn how to do so on this article:
https://developer.wordpress.org/advanced-administration/debug/debug-wordpress/
And if you need help to understand those logs, you can open a private ticket and attach the error log there, so we can help you with it.
Best Regards,
Salva.