To avoid dataloss, unexpected results, some actions have to be performed as preparation already before starting the upgrade.
Before the Upgrade:
First repair any inconsistent data still in the old release: Use report SU24_AUTO_REPAIR with all available options (documentation can be found in SAP note 1539556).
Initialize timestamps with report SU25_INITIALIZE_TSTMP (SAP note 1599128)
Create a backup transport of SU24 data after each step (you can use SU25, step 3 for that creation of the transport) and export it
Make sure, that the authorizations of your roles are actual. That means, that the existing authorizations should 'fit' to the existing SU24-proposals (i.e. Authorizations with status 'Standard' and/or 'Maintained'). To do that, start the 'Expert Mode for Profile Generation' in PFCG on the Authorizations tab and use the option ' Read old status and merge with new data'. This will start the merge function and will probably update the existing authorizations according the rules listed in note #113290. If you do not do that, you may be surprised about changes happening to existing authorizations after the upgrade during execution of SU25, where the merge function is used as well.
Create a backup transport of your roles and export it
Now after the Upgrade:
Apply all notes listed in note 440231. This note is kept actual with the latest notes.
Run SU25 2a-2c, alternatively you can use also the expert mode combining 2a and 2b by starting SU24->button 'Default Values Comparison'. As of 7.40 this expert mode is included in the SU25 action-list after step 2b.
<start of update 3rd Sep.2014:
The expert mode button is available in SU25 as of sapkb73112 in the button line of SU25 on the top.
Timestamp of step 2a:
Using the Expert mode, no timestamp for 2a is written automatically (so 2b, 2c won't work afterwards). Nevertheless you can set the timestamp with the corresponding button in the result list of the expert mode (as of note 2042284).
Attention: if you are using the 'normal' step 2a, do not leave the result screen with 'cancel' or closing the session, but rather use the back button to navigate to the su25 main screen. In some old correction levels no 2a-timestamp will be written, if you do not navigate back. (you can use the expert mode optne then mentioned above to set the timestamp then manually...)
end of update 3rd Sep.2014>
If everything is fine, create a final transport in step 3 of SU25 and transport the new proposals through your system landscape.
Then transport your already adapted roles as well.
Update June 19th, 2013:
If you have missed the first step of 'Before the Upgrade' (SU24_AUTO_REPAIR ->Repair Modification flags), note #1850378 provides a correction which corrects at least the SU24-entries with incorrect modification flags. Missing modification flags cannot be repaired anymore at this moment, as the old SU22-content before Upgrade is required to repair the missing ones.
Update December, 2013:
Please see also KBA 1954558
Update August, 2015:
Additional point 'Make sure, that the authorizations of your roles are actual.' added to section 'Before the Upgrade'.