i didn't see the request for original transcripts or LOR on the secondary. where do they request this information - was it upon receipt of your secondary?
as for the LOR, the following is from their web page:
Q: I am applying this year, can I send in my letters of recommendation before I apply?
A: Letters of recommendation that are submitted before they are requested, via the secondary application, will not be kept. You will need to resubmit them at the time you are completing your secondary application.