Dear Juan,
Then what you try to do is to upgrade from EHP4 to EHP6, you are not going to do a SP upgrade as I thought at the first time. In this case you should take into consideration that this process is more difficult than a SP upgrade and requires more time and effort. Everything should work as expected if you do all the process correctly and test the applications correctly.
Please take a look to the following documents:
SAP ERP 6.0 EHP 6 Master Guide
SAP ERP 6.0 EHP 6 Upgrade and Update Guides ABAP and Java
Software Update Manager Guides
Best regards.