I've changed the chiara local backup script to read a folder exclusion file, and excluded /users/public_html/detcharsummary, and things are working again.
This was neccesary because the summary pages are being updated every half hour, which is faster than the time it takes for the backup script to run, so the file index that it builds at the start becomes invalid later on in the process.
Thinking about chiara's disk, it strikes me that when we went from the linux1 RAID to a single HDD on chiara, we may have tightened a bottleneck on our NFS latency, i.e. we are limited to that single hard drive's IO rates. This of course isn't the culprit for the more recent dramatic slowdowns, but in addition to fixing whatever has happened more recently, we may want to consider some kind of setup with higher IO capability for the NFS filesystem.