If your version if anterior to 3.1, please have a look at the previous upgrade instructions.
Version 4.0 is a major release of the Alignment API. It has undercome many changes. However, these changes do affect the implementation of the API and not its interface. For a more precise list of all changes, please have a look at the release notes.
The change that should be the most frequent is that the Alignment API interfaces are expressed in terms of java.util.Properties instead of the org.semanticweb.owl.align.Parameters. Hence, most of the references to Parameters can be changed into Properties (and set/getParameter into set/getProperty). The org.semanticweb.owl.align.Parameters is morally deprecated and should be avoided.
We have evolved the BasicParameters implementation so that it extends Properties. Hence, if you use the BasicParameters interface, you can still use it.
The 2OMWG level alignments, provided by the mappingapi, have been discontinued and replaced by the integrated EDOAL language (identified as the 2EDOAL level). If you have previously used the 2OMWG level language and need to migrate, please, contact us and we will do our best to help you.
Please report any tweak that we did not mention here so that we can update this document.