CSV Import Suite Woocommerce

My problem is with upsells – essentially linking a base sku to other related skus. The problem is that the store I manage data for contains 150000 products. When I try to upload more than 1000-2000 skus worth of upsells they simply do not get entered into the database. When I shrink the batches down to 300-500 at a time they go through at a much higher percentage. The issue here is that I spend all day doing a task that should take 15 minutes. My boss, understandably, wants ALL upsells to be in the system as they are a sales driver and also look good. Is there a computational resource factor here, is there something I am missing or is this a common problem? Note – I am using the standard format for upsells and they work great in small batches.