How is the transfer handled in reverse? Does it apply the same percentages that were setup for the transfer into the investment accounts?

Transfers will also work in reverse. If the general HSA falls below the threshold, money will be transferred out of the investment area into the general HSA. The minimum threshold allowed is $1,000. Transfers can be turned off at any time by selecting “no” to auto-investment transfers.
The reverse transfer is handled pro-rata. This means that based off where your money is currently invested, it pulls the money out of the accounts by formula. For instance, if you are invested in two accounts at $500, it would pull equal amounts from the accounts. However, if you had $750 in one and $200 in another, it would pull more out of the $750 investment than the $200 investment. It is not directly tied to the percentages that were initially used for investment.