SQL Server: Duplicate Index Question
Without the execution plans, it's impossible to say, but I've seen a similar scenario pop up.  Had a client once whose database was teetering on the edge of being able to fit in memory.  Someone added an index on a large table, queries started using it (which kept big chunks of it in memory.)  Things all used to fit in memory perfectly, but they hit a tipping point where they started to hammer the disk much more frequently.  We caught it via the sudden spike in disk access and a sudden drop in Page Life Expectancy.

Ideally, you should capture these Perfmon counters continuously on database servers, and alert when they drop dangerously.  That'd help correlate things so you'd know if the PLE drop also happened, and that'd indicate you might be running out of memory to cache things.