Please follow this instructions when upgrading activeCollab to the latest release to keep the downtime of the system at minimum:
/activecollab and /public/assets folders are the biggest ones and it can take a while to upload them. That is why it's always recommended to upload them separately instead of overwriting existing files.
When you finish with the upgrade process, check if everything is working as expected. When you verify that everything is up and running, you can delete old versions of /activecollab and /public/assets folders, or keep them for backup, just in case.
This approach was proven to work the best and we use it when we upgrade activeCollab installations for our customers (as part of our Professional Installation and Upgrade service).