What sort of issues are you having?
I don't know iSeries, I work only with unix and windows. Each upgrade is unique, some don't any problems, some requires corrections.
I would suggest to test it in your test environment first, to have a first feeling how it will go.
Then prepare for production, were you might have the same experience as the test. Or as I experienced sometimes... some new issues! In that case a backup of the cmod system tables are quite handy for a fall back scenario.
Maybe I was lucky but with my 8.4 -> 9.0 I had no issues so far...
Let see the next one, how it go :-)
Sincerely yours,
Alessandro