We apologize for your trouble, this is obviously not the kind of experience we are looking for, but we also cannot account for what other add-ons may do with our citations. Thank you for highlighting this possible explanation.
Luckily, Google Docs has built-in versioning, so you can fix the loss of data by going to File --> Version history --> See version history. Then find the latest version where the citations are intact and restore that version. The “citation data” we store in the document are just links (urls) and so are very unlikely to not be saved in the document’s history.