OK, I think I follow what's happening. You want to modify a document that was saved in Acrobat with an extension. You open it in LiveCycle and get that error message. That's alright, probably. It's very similar to the error I get on ES2: "Some usage rights have been applied to the form you want to open. Opening the form will remove the usage rights. Do you want to continue?"
Try this and see if it works. Open the document in LiveCycle (you may have to "save as..." like it says), and make your modifications. Then save the document. Open the document in Acrobat and Save As > Adobe Extended PDF... or whatever the menu option is, now. (I think it changed slightly after a recent update.)
My apologies, here is a bit more of the background. I created two separate documents in LiveCycle. Both documents are dynamic forms with expanding text boxes. Originally, the forms were in an Excel workbook and you could tab to either form (as someone might use one or the other, or both). To mimic the nature of the Excel workbook, I have packaged these two dynamic forms into one PDF package so that it is able to be viewed using only Adobe Reader. The intent was to create bookmarks so that the user could still tab to one document or the other. I was attempting to create the bookmarks in the user PDF version and it was not allowing me to. Does this clarify?
You can try to add the bookmarks in Acrobat before you save the package as Reader Extended file.
But I don't know, if the bookmarks will work, because the targets in a dynamic form does not exist as long the file has not been opened.