It can take about two days to do such a big upgrade, with time being spent on making backups of the database and file system, and time spent organising all of that!
Noticable changes on Kentico's part:
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Some changes in the API (documented - read the entire PDFs supplied)
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File system changes (substantial between the versions)
Change in practice: Upgrading from 5.5 R2 to 6.0 involves a change in upgrade practice. Up until 6.0, one performs all upgrade actions manually, ensuring to follow
very carefully the upgrade instructions, checking
every page. Going to 6.0 is done by way of an application (supplied by Kentico).
The great thing about version 6 installations is the new install utility that takes care of all the backups and easily allows hotfixes to be applied. One nice feature that has been introduced in version 6 is the ability to tie scheduled tasks to the operating system and the install utility makes implementing this feature a breeze.