Why opening a PDF with Illustrator gives wrong results?

The issue is that Illustrator can only be trusted to successfully open PDF files that were produced by Illustrator with the “preserve Illustrator editing capabilities” option turned on (which includes an .ai version of the file inside the PDF).
When opening a foreign PDF, Illustrator may or may not be able to do.
Also note that When a PDF file is saved with "preserving the editing capability" in Adobe Illustrator, some kind of private data are stored in the PDF.
Any correction on the PDF made by tFlow or by any other pdf tool, will only have an effect on the PDF part of the file - not on the proprietary Illustrator data.
So when the file is opened in Illustrator later, this software will use the (unchanged) private data representation of the file - and not what is "really" included in the PDF part.
This means that some changes applied to the PDF will be not visible when the PDF is edited in Illustrator or rendered in a different way.
To view and edit a PDF the proper tool is Adobe Acrobat.
Please find here some useful information: