I have requirement of read a file from fileserver and delete all records from Database if filename is present in database. Next step is to load data from this file.

This is more like delete/insert. I cannot do upserts because the new file can have more/less records after correction from the source.

Does anyone have idea to this?

I tried Fetchfile ->ExecuteSQL- PutDatabse. 
I will loose the file in this case after executeSQL.

Have idea of placing funnel in between and do fork but delete might take time before file starts processing.