I've been running Zimbra on Ubuntu for some time, and I haven't had a problem with APT upgrades. In fact my system is current as of this weekend because I did an APT upgrade this weekend prior to my 5.0.18 upgrade. I've never had an issue, but should always make sure you have a backup prior to any major upgrade.
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Release 6.0.2_GA_1912.UBUNTU8_64 UBUNTU8_64 NETWORK edition + Mobile Option
Activesync with Moto Q9C, HTC Touch Pro, Palm Pro, & Palm Pre
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