When I add a Pipeline directive to the DCT_Inner_Loop of the (UG871) Lab1 design (attached) and remove it, the C code gets changed as shown below.
This behavior is seen only with Vivado 2013.4 and does not occur in 2013.3.
Try to change the modified code manually and give the directive again.
There is a chance that you may not find the DCT_Innner_Loop in the directive pane, but this occurs randomly.
When you close and open the project and make the manual changes, you can synthesize the project.
This issue has been fixed in Vivado 2014.2.