Exporting a PDF changed the colour of a logo - why?

Are you working with the original InDesign working document? What does the Pantone 2955 CVC look like in your Colours palette there? If it's Pink, then you need to reimport the proper definition from the logo file.

Normally I would say, open the Illustrator file for the logo and recolour the file with the current Solid Coated 2955 C, but since your client is already peeved, they may not like THAT shift in colour, so let's work with the CVC version:

Based on what's in your PDF, the only thing using that colour is the logo, so temporarily Cut (Command-X) the logo. This will free up the Colour Pantone 2955 CVC in the list. Delete that colour. Paste your logo back into position. This will reimport the colour from the file. It shoud be Blue now.

btw: "I'm using a custom PDF export setting that forces everything to CMYK."

You shouldn't have had spot colours in the PDFs at all, then. Both of your samples do, so we should see exactky how you have your settings.

You should also look at updating and considating your Pantone colour usage in the document.

You had 3 spot colours, two of them 2955 with different definitions, but I assume all are supposed to be the same "corporate" blue. The question is, which one should to go with? You SHOULD go with the latest method going forward, so that would be the Solid Coated "C" that is LAB based, and this will convert to CMYK dynamically according to your Color Management settings. There is also the Color Bridge Coated set "CP" for a newer fixed defined CMYK mix that Pantone has put its stamp on, but I find them weirdly off on some colours, so I usually avoid it.

It should be noted the CMYK mixes in the old CVC set are quite a bit lighter than what you will get from converting the Solid Coated set, because they were measured based on old-world printing processes where there was a great deal more dot gain throughout the process than what we get today in modern direct-to-plate imaging. e.g.:

It appears for whatever reason, the 2955 CVC spot colour was redefined or remapped in your InDesign document.

This normally wouldn't be possible if a logo was already placed; ID locks out editing of placed colours. But it IS possible if that graphic was deleted - You can then edit the blue in ID to something else, in your case the Pink (approx 89M 14Y). So, even if you re-place the logo, it will look Blue, but it will print in the Pink as now defined in ID.

Why would someone do this? I can think of some reasons, but I'm going to assume this was accidental.

In any case, once you've fixed this: If you are providing a PDF of an ad for print that is meant to print only in Process colours, you should "change" all your colours in your ID document to Process in your Ink Manager, BEFORE you make your PDF. This avoids the possibility of sending spot colours down the line, and also a good way to proof the final thing on screen (but yes, if you had looked at Separation preview in either ID or Acrobat, you would have seen the problem)

(fyi: CVC indicated the old school Pantone Libraries that were used years ago and were based on Process Ink Mixes, as opposed to the LAB based mixes used nowadays. It was defined as 100C 43M 0Y 34K.)

Can you share the PDF? A shift from blue to pink wouldn’t like be caused by Color management or profile assigments.

1. What file type has the logo? EPS does not support color management, rgb will change anyway. Best is AI or PDF/X-4.
2. What color has the logo? Spot color, RGB with color profile? When spot color, what policy did you apply? 
3. If the logo was in CMYK, did it have the same color profile as your print, or a differen? If it was a different profile, which policy did you choose for output? Keep values, ignore, or convert to destination?