Dropping table indexes prior to using the MERGE utility

I am being asked to change the processing done when updates are being applied to the database.
Process:
1. Initial data load - Use SQL Loader to load the main database tables.
2. Daily data load - Use SQL Loader to load records to temporary tables and then use MERGE utility to insert new records and update existing records in the main database tables. Just prior to starting the MERGE utility, I drop the indexes on the main database tables. At the end of the MERGE, I re-create the indexes.
The problem seems to be the application using the database can't handle the queries if the indexes are dropped and being readded.
Does anyone have any ideas?

I am currently dropping indexes because when the MERGE processing takes place, it can insert new records or update existing records (based on the primary keys matching).
When I started to use the MERGE, I don't think the update was successful because the primary key constraint. So I disabled the primary keys indexing and other contraints during the MERGE. Then recreated at the end of the MERGE. Perhaps I need to revisit the information for MERGE.
I don't have any real benchmarking other than the application developers indicating that they experience the application processing delay during the daily load. I've thought about loading into a shadow table and rename at the end of the load but it not really be possible now.

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