Hi, when you do the upgrade, it actually creates a new database and migrates all the system information over. Event information is migrated over if you want to as a post upgrade task. Is it important to you to migrate the event information over. If not, then you may be able to miss this step and save some space on your SQL server.
A new database called epo4_<ServerName> will be created.
Make sure you read the EPO 45 manual about the upgrade, there are some good points to be aware of around supported products.
One step I have seen some customers do, is build a new EPO 3.6.1 server, and attach a copy of the production database to it. Once you have confirmed its connected OK, then run the EPO 45 upgrade on that server. This will give you a good Idea on whats happening during the upgrade. How well the data migrates, and what your system tree will look like once the upgrade has taken place.
The timeout problem here is most likely caused by the productevents table being too large rather than a particular problem with the events tables. However, it may not be as serious a problem as you think :-)
The upgrade to 4.5.1 doesn't update the existing db - instead it creates a new db and migrates the data over to it. The event data is not migrated by default - instead, you run a one-shot migration task after the upgrade is complete. This migration task should only migrate valid events - so you shouldn't really have to worry too much about straightening out the events if you're intending to upgrade.