I've made this discovery a few months ago and I've been trying to soak up as much knowledge as possible, from the audiobook to the podcasts. 

Sometimes they are just discoveries in progress (like opening up a wall and finding bad wood or wiring), other times, the owner will change their mind and request a different tile of a nicer countertop, Etc.But regardless, the Contractor must execute a Change Order and present it to Owner for approval before proceeding.

If yes, you will be collecting that directly and need to engage your tenants...I'm a little perplexed...it's standard practice for me as an agent to plan the takeover weeks before we close...we engage the housing authority before closing and deliver a tenant engagement letter on day 1...there is a lot of up-front discovery with HAP contracts and validating property performance in general (due diligence)...if you used an agent for your transaction, they have set you up for failure...it's pretty common with unexperienced agents, but lessons learned...Do you have a PM? 

A lawyer could probably tell you if your seller’s lawyer has to tell the first seller’s lawyer about his/her discovery that there was no actual lose.

We disputed the overage because they did not notify us before hand.He provided a slight discount bringing the overage down to $2000 (~20%) over the estimate, but basically says we are on the hook for the overage and that he had no duty to submit a change order since the scope didn't change (although the discovery of excess roots seems like a scope change).

I would have to go through the whole discovery process and prove the legality of the unit in question.

Perhaps do some discovery on the listing agent and find a common ground.

Fast forward 10 years the sheriff knocks on my door and I discover I have an opportunity to gain control of the house for 4K taxes.

Probably not much depending on the price point, inventory is still tight and a lot of people will see that as temporary, there is someone for every house, don't be scared to do a little price discovery before dropping price.

Here is a simple and fast read, should assist in getting your wheels moving on the discovery portion of your process: A Simple Guide for Buying Out of State Turnkey Investment PropertyAlso, keep in mind you will want to define a lender that is investor friendly, as with any business, banks are also not all made equal, define a lender who is investor geared, at minimum one whom had worked or works with investors as part of their core business.Happy Investing