The version is shown in the $SCHRODINGER/knime-v*/ (where * is the version number). I am glad you have found a workaround. We have changed the Include Input parameter in Ligprep (and other nodes) to "Output Column Structure" which allows you to specify the output (i.e., Input plus Output, Output replaced within Input columns, or Output only). Together with the Match Input option, these options make it a bit easier to understand what to expect in the output columns.
If you do want to use the Input data in your current version, you can use the "Lookup and Add Columns" node to do so.
Hope this helps.