CX2 should handle correctly ISBN rather than putting nowiki tags around them, either with the ISBN template, or just plain text (and letting MediaWiki do the magic links if it's configured to do so)
Example
Example on frwiki "Conservation russe" : original translation, manual fix
When translating Русская беседа from Russian to French. The bibliography section has an ISBN code in the original article that is presented in different ways: in the original article it is shown as an "ISBN Link" in Visual Editor, and as plain text "ISBN 978-5-211-05327-4." string in wikitext. In Content translation it is rendered as a regular link for the source document and adapted as an empty link in the translation. Finally, when the translation is published, it results in "<nowiki>ISBN 978-5-211-05327-4</nowiki>".
Empty link shown when added to the translation:
Link on the source document:
__
Related: