Migrating orders doesn't migrate total values
The bi-directional link is a relic of the Drupal 7 entity API at the time we wrote Drupal Commerce 1.x. It was basically a DX concession of dubious benefit, but we'll be fixing that in 2.x. ; )

As for how order totals are calculated, order save automatically calculates the total by summing up all of the price components in the "total" price fields on line items. If you haven't properly set the associations in your line items or if you haven't set the price component arrays for the line items you've created, your order total will not calculate properly.