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Whenever it's time for you to upgrade modules on your site, you should have a checklist of the steps involved. One step I've recently added to my checklist is to clear the site cache just prior to uploading the updated module files.
I learned this lesson with a recent Views upgrade. While working on my dev server (#1 on my list!) I found that if I didn't clear the cache prior to installing the updated Views module, I was faced with the dreaded White Screen of Death (WSOD to those of us familiar with it). After a few minutes of my time in the Views issue queue, I found other people with a similar issue and the result was consistently some type of cache-clearing activity. Once I reinstalled the old versions, I cleared the cache, reinstalled the new versions and all was great.
For the record, here's my module upgrade checklist:
Did I miss anything? Do you have any additional steps in your module upgrade checklist?
Haven't ran into that
That's not a problem I've ran into, but good info to have.
I keep all of my sites (and clients' sites) in SVN and have found that occasionally I have to remove all of the files from the local working copy before updating modules to catch files that are removed or renamed.