Here are the major changes:

The fight:

The shopkeeper gained some moderate resistance boosts (i.e. health, stagehp, and armor). Expect a longer fight.

The shopkeeper's summons got switched around. 1-2 coins spawn instead of 2-4 and 3 greed gapers spawn instead of 2.

In default circumstances, 2 shopkeepers will spawn instead of 1 if you are in depths I and beyond. Stealing right before womb just got harder.

The aftermath:

The original behavior of the next shop being worse and then recovering the stage after has been replaced. Now, an RNG roll determines if you will be forgiven each stage. This forgiveness will improve the shop by one stage, so if you had a poop shop because you escaped the fight, you will get a pickup-only shop if you are forgiven. This process will repeat until you are back to a normal shop.

What does this mean? If you are lucky, you might see your shop get better on the floor immediately after the one you stole on! Yay! Worst case? You might not see a normal shop for a while.

If you are going to have a poop shop, there is a 33% chance that it improves to a pickup shop, increasing by 33% each floor until you are forgiven.

If you are going to have a pickup shop, there is a 25% chance that it improves to a normal shop, increasing by 25% each floor until you are forgiven.

Note: you will not know if you have been forgiven until you enter the shop to check. You will be notified with a fortune (and an improved shop) if you have been.

With the recent update, stealing from a shop also increases all future prices of items by 20% for every item you have stolen.

Finally, if you have stolen an item, if you steal again, an additional shopkeeper will spawn for every item you have stolen before. For example, if you steal in basement I, and then steal again in basement II, you will be faced with 2 shopkeepers instead of 1. If you steal another time in caves I, you will be faced with 3 shopkeepers. There is a cap to how many spawn that is set to 3.

As for additional fixes and things:
There is now a death screen sprite for the shopkeeper.

How the timer is rendered has been reworked.

The changes made to the aftermath behave correctly when switching between the alt and normal paths, so you should expect logical behavior when going between them.