Tom's right in his suggestions (as always).
I definitely wouldn't start with pump-seals and check valves. Changing to 100% water should not have caused any harm to any part of the instrument. If the water was elderly and had some microbial growth then it could start to block the little filter in the purge valve, but if it's bad enough to do this in a matter of an hour or two, then you would also see a lot of greeny-yellowy mess on the inlet filter in the bottle itself.
Partial increases in back-pressure aren't typical of check-valve or pump-seal problems. Outlet check-valves, if they get stuck closed, cause total loss of flow and infinite back-pressure, not a gradual rise with changing gradient conditions (with the exception that some designs get stuck more often in 100% ACN than other solvent compositions). Inlet check-valves, if stuck shut, mean that at best the pump is sucking a vacuum and re-filling it, which tends to look like low rather than high pressure. Pump seal problems never cause increased pressure (in my experience, so far); they cause puddles, wandering retention times, and ultimately missing peaks.
What I have noticed is that often we tend not to remember what our system looks like, until it goes wrong - sometimes quite a small mistake just tips it over the edge, when in fact it's been going wrong for a long while - or a minor change exposes an existing problem. I suspect that running slightly dirty water for an hour or two was the straw that broke the camel's back, but the camel was probably already close to breaking-point.