Understandably, a CIM generally paints any company in the most positive light, with any skeletons neatly tucked away in the closets. I'm not accusing brokers/owners of any impropriety, just the way this goes.

Inevitably, diligence may/should uncover issues that need to be considered. In the case that these issues become material factors in the deal, how have you addressed with the Seller? And probably more specifically, when have you addressed them?

On one hand, it would save time/money to address (and possibly renegotiate) an issue as soon as it becomes known.

"Woah, [this new thing] changes my view of the company quite a bit, I would need to change the terms [in this particular way] in order to continue feeling comfortable moving forward. And by the way, there's still more diligence to be had and we may need to address any other items that come up in the future."

On the other hand, if there end up being a few different issues, it may make sense to wait to have a clear picture of the entire business:

"...Throughout the diligence process I've developed a clearer understanding of your company. When I submitted my offer, I wasn't aware of [A], [B], and [C]. They represent certain risks that I think we could address via the following adjustment to the deal terms..."

Obvious challenges with both approaches, wondering what has worked best for you? Keep in mind, I'm not implying a strategy or tactic to simply lower the purchase price after entering LOI. Assuming there are genuine new reasons for concern, not enough to kill the deal though, and negotiating in good faith.