What flattening JavaScript did you use, exactly? Note that Reader usually cannot actually flatten a form (exceptions for some mobile versions and when using EchoSign functionality in desktop versions). The doc.flattenPages JavaScript method does not work with Reader, even if the document is Reader-enabled.
Regarding the date, you probably have a script that set the field value to the current date when the document is opened. If you want to prevent this, you'll have to modify the script so that it doesn't change the date field if the form is filled-in.