Most likely there is blocking. Can you check sys.dm_exec_requests when there's load and see what the query is waiting for?

You don't.
Insert the row into the remarks table, obtain the ID assigned to that row, put that into the customer table.

Then the necessary permissions were added for the account when the login was changed.

That's not going to work for what you want. That query, if there are ANY rows in employee with ID between 1 and 2000, then the insert won't run.
You...

Then you'll need to use option 2.

The answer for 2) makes no sense, you can't update when rows don't exist in one table. I'll assume you meant 'insert them' for (2) and 'update to make the...

What, exactly do you want to do with the rows that are:

1) In employee, not in backup.employee?
2) Not in employee, in backup.employee?
3) In both?

I'm confused.
You say you want to update this table from another DB, but the query you're running is an insert, not an update.

The reason you're getting the ...

Please note: 3 year old thread.

What was confusing was your use of 'query'. A script (multiple queries) executes top to bottom, a single query doesn't.