On my rooted Incredible I was able to resolve this with ADB:
adb shell
su
cd /data/data/com.htc.android.mail/app_mail
rm *
I suspect this directory is wiped during a system reset, so this approach just allows all the other phone apps and settings to remain unchanged. After performing the above commands, my Mail size (as reported in settings -> Applications -> Manage Applications -> Mail) went from 112MB to 2MB. All of my Mail Accounts and settings remained intact through this process , but downloaded mail was wiped out. Since I don't delete from server, my mail from today just downloaded again on the next sync.
adb shell
su
cd /data/data/com.htc.android.mail/app_mail
rm *
I suspect this directory is wiped during a system reset, so this approach just allows all the other phone apps and settings to remain unchanged. After performing the above commands, my Mail size (as reported in settings -> Applications -> Manage Applications -> Mail) went from 112MB to 2MB. All of my Mail Accounts and settings remained intact through this process , but downloaded mail was wiped out. Since I don't delete from server, my mail from today just downloaded again on the next sync.