You can replace documents if required, preserving your work product. To do this for a single document, right-click and select Replace:

Choose the file and Opus 2 will determine whether it is a PDF or Native file. When you select Next it will then produce a comparison against the previous document, highlighting which annotations (if any) will not be carried across if you select the Replace button:

If text on the original version is no longer available on the updated version of a document, then any annotations will transfer across in roughly the same location but will not be exactly mapped as they do not have the text to anchor to. If the document has been OCR’d and the text is still available on the updated version, even if it is not in exactly the same place, the annotations will map to the text and be carried across.