Tim,
I have had a read of your blog post and have experimented myself to see if i could reproduce your issue. Curiously, I couldn't. I have sequenced an app to c:\program files\<app name>, opened for upgrade, made no changes, saved it and
launched this new version on the client. No problem!
Because this issue is only relating to 4.6 SP1 maybe this issue has something to do with the new symbolic link functionality on the sequencer? Do your machines have real Q: drives or the new symbolic linked ones?
If you use the new option to "Expand Package To Local System..." before you open the sequence, does this work around this issue?
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