It's shouldn't give a problem, but that is a lot of small inserts! Unfortunately, I've never seen and SqLite version of the SqlBulkCopy class, but it might be worth doing it as a monolithic single insert operation via parameter blocks - there is an example here: http://procbits.com/2009/09/08/sqlite-bulk-insert
] which may help.
I've never tried to add 400K records in one operation, but it should be well within the capabilities of SqLite. It's worth trying a parametrized version just to reduce the number of file accesses - that may cure the problem.