I have an idea to throw at you. You said that you were going to add the 139 missing players from last season AFTER waiting 10 days or so of this Free Agency frenzy.
Why not reverse that & go ahead & add those missing players & then in about a week to 10 days you can do the updated transaction from FA for another roster update?
I say this because it's best to just add the missing players first because the Free Agency action will just be a mess to keep up with the next 10 days-2 weeks anyhow.
Just don't worry about transactions starting from tomorrow through whenever you get the 139 missing players added to the roster. Then, once the 139 players are added you can update all the transactions again from the time you had stopped from before.
To me as a former roster creator myself would be the easier & more simpler way of going about this. Of course, it's your roster & in the end it's your call but I wanted to run what I was thinking by you. Thanks.