Even normal aircraft, no matter how venerable and reliable, can (and should) undergo modifications if something can be done to improve safety, reliability, ease of maintenance, etc.
A good bit of the work I did in the air force was to perform modifications and upgrades, as well as normal maintenance, to the ejection seat systems (mostly for the ACES II, which has been around for a while). Some of the modifications were to eliminate potential flaws that might endanger the crew member under certain ejection conditions. The odds of those conditions occurring may have been small, but maybe a recent ejection exposed the flaw, and it was prudent to take action to correct it.
Spacecraft are no different, really. They come off the manufacturing floor as the best design that can be envisioned at that time. With a few launches and experience, you start to see things that you *wish* you thought about before. And so you make a modification to remedy the problem in existing ships, and you work it into the design of new ships. These modifications are the cost of doing business in a good organization. It can be expensive, but it's always cheaper than killing crew and losing ships, *then* making the modifications anyway.