Apparently there is a bug when trying to programmatically change the links in the Summary Link Web Part. I tried checking out the page first ( pageFile.CheckOut(); ). I tried allowing unsafe updates (spWeb.AllowUnsafeUpdates = true; ) and I also tried updating, checkingIn, and publishing:
pageFile.Update();
pageFile.CheckIn("Updated by LinkUpdateTool");
pageFile.Publish("Updated by LinkUpdateTool");
None of which worked...
I was adding the links using: << linkWP.SummaryLinkValue.SummaryLinks.Add(linkItem); >> where linkItem is a SummaryLink object.
I looked up a bunch of code examples online but couldn't find anything else to try so I started playing around with ordering of the function calls to no avail. I then dug deep into a google search and found a single line of code which resolves an apparent bug in the API:
linkWP.SummaryLinkValue = linkWP.SummaryLinkValue;
Do this after you add your new links but before so save the WebPartManager. Ie...
wpm.SaveChanges(linkWP);
Frustrating but so relieved I got it working!!