Hi @iybar,
I tested your code and was not able to reproduce this issue. Can you confirm the annotations are actually being flattened? When flattened onto a document, the annotation data will no longer exist in the annotation manager as the annotations are technically now “burned” onto the PDF; you shouldn’t be able to select them/move them.
Please also ensure that you have enabled the fullAPI as it is required for flattening.
If this does not resolve your issue are you able to share the version of WebViewer you are using? Also, which demo are you able to reproduce this on? I was not able to reproduce this in our flattening demo either: