I ran into a situation today where I was switching out the domain account associated with a data source in the Forms settings, but I hadn't properly configured access in SQL to all the necessary tables/views/stored procedures in the target database. Instead of warning me anything was wrong, Forms happily updated the connection information and gave a small popup notifying me that some of the tables/views/procedures appeared to be missing and that it had deleted any lookup rules referencing those objects. Fortunately I had a backup of the database, but I was quite shocked that it behaves this way.
It is also a major inconvenience to export/import forms in situations where the database name or connection information on the import side is slightly different than on the export side. We run into this all the time if we develop a solution that uses lookup rules for a customer on our own test systems, then try to deploy it on their production system. All of the lookup rules get deleted on import if the data source doesn't match what was on the export side. The only workaround I know is that you can manually edit the XML file before importing to reflect the changed connection information.
Please consider deactivating or flagging invalid input rules on the form without deleting them automatically. It would be great to give us a chance to correct any permissions/connection profile problems before just assuming the rules need to be removed.