inDesign Link Fail

[ELPrepress]

I was working on this handout and they have just put up a new building.  After the first proof they asked me to Photoshop out some of the building lumber and plastic still visible in the photo. I did that. Updated my AI file with the type and new photo. Sent the proof. They liked it so I opened inDesign, told it to refresh the updated links and output the pdf.  What I didn't notice was that the file never updated in inDesign. In fact I can't make it happen.  I even clicked the edit icon to make sure that I hadn't saved a copy of the old version somewhere, but no what it is linking to just plain doesn't match what it is showing! My mind is blown on this.  I can't figure out how this could possibly be pulling a file that was overwritten and therefore no longer exists instead of what I want.  Here is a screenshot:

Notice the wood in the windows and the light spot on the gray brick on the right.

I was doing a different job earlier today and when I relinked a file it said that it had the label for the King bed mattress as a current link, but my layout still obviously had the Twin label showing in the body of the layout.  I didn't save the file and restarted the computer and that layout appears to be working but my church card file is still messed up.

Any ideas? Is this a known bug?  Running on OS X Yosemite 10.10.5

[BobLevine]

Almost certainly user error. If the link shows as up to date in InDesign than you probably have two different files floating around.

[ELPrepress]

I would expect that by clicking the edit link button that the file that it would open would most certainly be the one that has as linked in.  However as you can see in my image it most obviously is not.  I have also verified the actual file location which is also identical.

[kevin stohlmeyer]

Replace the image altogether and check your Place options. You may have custom selected layers with "keep layer overrides" activated, meaning no matter what you save InDesign is overriding your Photoshop preview.

Another way to check is select the image and go to Object/Object Layer Options and check the layer visibility and selection at the bottom of the dialog box.

[ELPrepress]

I linked to something random and then went back to the file in question and it did not help.  I have checked layers in each of the files but on one layer is the building image itself and the other contains the type.  It isn't a issue of the wrong layer being visible.

[kevin stohlmeyer]

Move all the files associated with this to another location and purposefully break all links. Then relink to the asset in question and see what happens.

[ELPrepress]

This appears to be another case of where the pdf data which apparently is used when linking files is different then what it is when actually opened in Illustrator.  After mucking around with linking and relinking and moving files I went to recreate the print layout in AI and found that I could get the same error when linking it into an Illustrator file as well. So I tried opening the ai file in Adobe Acrobat and I get the deprecated version which doesn't match what shows when the file is opened in Illustrator.  It is not the first time I have had this bizarre error, but I had not encountered it in a few years.