If PDI does not recognize changes you made to a table, you need to clear the cache of database-related meta information (field names and their types in each used database table). PDI has this cache to increase processing speed.
If you edit the table layout outside of Spoon, field changes, deletions or additions are not known to PDI. Clearing the cache addresses this issue.
To clear the database-related meta information cache from within Spoon:
Select the connection and then
Clear Cache. Or,
Database connections >
Clear complete DB cache.