Don't assume importing data is as easy as dumping it in your database and having the computer handle all the processing work. As you've discovered, an automated load can have problems.
First, database ELT processes depreciate the hard drive. Do not stage the data into one table prior to inserting it in its native table. Your process should only import the data one time to its native table to protect hardware.
Second, you don't need third-party software to middle-man the work. You need control so you're not manually inspecting what was inserted. This means your process is to first clean / transform the data prior to import. You want to prevent all problems prior to load by cleaning and structuring and even processing the data. The load should only be an SQL insert script. I have torn apart many T-SQL scripts where someone thought it convenient to integrate processing with database commands. Don't do it.
Here's how I manage imports from spreadsheet reports. Excel formulas are better than learning ETL tools like SSIS. I use cell formulas to validate whether the record is valid to go into our system. This result is its own column, and then if that column is true, a concatentation column displays an insert script.
=if(J1, concatenate("('", A1, "', ", B1, "),"), "")
If the column is false, the concat column shows nothing. This allows me to copy/paste the inserts into SSMS and conduct mass inserts via "insert into table values" scripts.
If this is actually updating existing records, as your comment appears to suggest, then you need to master the data, organizing what's changed in logs for your users.
Synchronization steps:
Log what is there before you update
Download and compare local vs remote copies for differences; you cannot compare the two without a) having them both in the same physical location or b) controlling the other system
Log what you're updating with, and timestamp when you're updating it
Save and close the logs
Only when 1-4 are done should you post an update to production
My guide to synchronizing data sources and handling Creates/Updates/Deletes:
sync local files with server files