AppGratis CEO Simon Dawlat has published a blog post explaining exactly what led to the app’s removal from the App Store. The removal was indeed centered around the violation of two of Apple’s App Store rules, especially one limiting promotions via push notifications.

Dawlat says that AppGratis had been rejected for publishing in the fall of 2011 for a rule governing the duplicate publishing of very similar apps in the App Store. At the time, it also fell afoul of the new (at the time) guideline 2.25 limiting stores from presenting promotional apps in a way confusing to users.

AppGratis was later able to get the app approved, even under the new 2.25 rules, and version 3 was published in late 2012. A version of the app for iPad was also approved less than a week ago.

“And then last Friday, a few days after Apple had approved our latest iPad version, a new App Review team member named R.,” says Dawlat, “who no one on my team had ever had contact with before, came pretty much out of the blue and after trying to call me three times without being able to get hold of me (I was on a plane), decided to pull out our apps because of guideline 2.25 and also – re-gasp! – because of guideline 5.6.”

The only push notification that Dawlet says the app sends is a daily opt-in-only ‘Today’s deal is here!” message pointing users to a sale.

Dawlat was unable to change Apple’s mind about the rejection:

Initially, I thought we’d been caught in an internal communication accident and not the victim of a supposed “ban on third-party apps.” We checked the apps of our competitors, all of them were available for download. All the lights had been green for the past few months with Apple, so it seemed very unlikely that such a company would change its mind pretty much overnight, in what looks today like an extremely volatile action.

Early Monday, R. gave me a follow-up call. He basically couldn’t go beyond repeating multiple times that our app had been pulled out due to guideline 2.25 and 5.6.

I asked how he and his team could have possibly changed their minds overnight, pretty much pulling the plug on a 45-person company. He seemed very detached regarding the gravity of the situation, and was unable to let me know on what specifics these decisions had been made.

Over the weekend, the news broke that the app discovery tool App Gratis had been removed from Apple’s App Store. After reaching out to Apple, the company informed us that the removal was due to the violation of two rules, specifically:

2.25: Apps that display Apps other than your own for purchase or promotion in a manner similar to or confusing with the App Store will be rejected

5.6 Apps cannot use Push Notifications to send advertising, promotions, or direct marketing of any kind.

The first rule has shown up in stories about app removal before. Specifically, back in December, Apple removed the App Shopper app from the store for violation of 2.25. In the case of AppGratis, the removal is really more about the second of those two rules, as it had been sending push notifications with promo deals on apps.

Though some of the stories about the removal of AppGratis have focused on the first rule, it’s important to note that AppShopper did not do the latter, and it has yet to be re-admitted into the App Store. AppShopper publisher Arnold Kim confirmed to us that the removal was specifically about the new 2.25 rule that Apple added back in September which governs the promotion of apps not your own inside your apps.

In other words, this isn’t just a matter of causing confusion by mimicking the feel of the store, which is what 2.25 was designed to prevent.

AppGratis closed a $13.5M round of Series A funding in January. At that time, it said that it was earning more than $1 million in monthly revenue and had 7 million users in over 30 countries, Dawlat now says that there are 12 million users.

“And that is pretty much where we stand,” he wraps up, “still stunned that Apple took the decision to destroy so much value within their own ecosystem, but more than ever convinced that what we’re doing is good, and accomplishing a much needed mission in a broken App Discovery world.”

He urges Apple to reach out and people to share the story. Currently, neither AppShopper or AppGratis is available in the App Store.