Improving readability and logic on "re-indexing" method
I have the following comments and recommendations:


The try/catch is too general: if anything goes wrong anywhere, you return false. This may mask errors. Catch more specific exceptions and narrow the scope of your try/catch to where you are okay with things going wrong. (If you don't EXPECT anything to ever go wrong in certain parts of the code, you probably want to "fail fast" and catch that exception at a higher level. This could hide lots of kinds of errors during dev/test.)
Name mismatch: requiredIndex does not match .SortOrder (I'm not saying they need to be same exact name, but these seem to describe different concepts to me)
Does .SortOrder need to be optional? Consider enforcing that it be set by changing the orginal OutputTemplatePage class to require it. Is it an enum? If so, perhaps the default value could be Default (as in "use the default sort order")
Name choice: Boolean boolHasBeenAdded might be better as Boolean pageHasBeenAdded (prefix notation has been out of vogue for years - since .NET, certainly). Also, I usually prefer language types (bool) to the .NET types, but that's just style/preference.
This block could go away if you invert the next conditional (since this block happens anyway at the end): 

    if (items.Count() == 0)
    {
        Add(page);
        boolHasBeenAdded = true;
    }
    else



... to ...

        if (items.Count() != 0)



Consider moving the following code into a well-named helper method to make its intent more apparent:

            OutputTemplateRepository repo = new OutputTemplateRepository();
            OutputTemplatePage pg = repo.GetOutputTemplatePageById(template.Id);
            pg.SortOrder = ctr;
            repo.Save();

It is unclear to me what repo.Save() does - seems like it might have side-effects. All the more reason for prior suggestion.
Rename ctr to something more descriptive. Is it the sort index? Of course, setting SortOrder = ctr makes me wonder if SortOrder is named correctly. "Sort order" makes me thing of high level approach to sorting - like ascending vs. descending? Not clear. Makes it hard to grok.


[Edit] Actually, this largest problem might be that this code is not in the right class which might be the source of some awkwardness. Consider making ReIndexOutputTemplatePages a method on OutputTemplateRepository to clean up the code leading up to rep.Save.

Hope that helps!