"Commercial aircraft do not undergo major upgrades every few years where most of the interior is removed, equipment and structure inspected and upgraded"
Yes, they do. Boeings commonly have C & D checks at which seating positions are often changed. This type of modification, as you should know, means Primary Structural changes to the whole airframe to protect the passengers new positions.
And because civil aircraft of the same type do so many different flight profiles the inspection severity and periodicity is adapted to suit each particular airframe and/or operation. This could mean that civil aero-maintenance companies would reduce the inspections of (as Nova Nav implies) low-use airframes because over-maintenance is also a waste of time and money. The military "norm" (from my past experience) is to continue with whatever (single) maintenance policy is published/available whatever the use of any airframe within any fleet - a really big mistake in my humble opinion.
Another major principle of PRACTICE states that, if you keep messing with structural loadings you will eventually weaken some part of it in a way you did not intend...
By the way; I have no doubt that all of the employees at Boeing, L3 and all those others trying to ensure the best outcome of these events are doing their utmost, honest and best work. I am just trying to put across the notion that even the best of intentions sometimes has unexpected outcomes and old aeroplanes are old aeroplanes whatever the work conducted on them.