I have checked the conditional text, notes and assignments. I did find an InCopy assignment but it is not present in my document. I did not find it on Links nor in any other part of the file. When I am opening InDesign original file it did not ask for a missing link or anything.
As I said this is the first time I am encountering such error. In the end, I copied the English text into a new InDesign project and exported it as IDML. The new IDML is clean and no more other languages are present except for English.
Regards,
Sebastian