Here’s the good news – in the short term nothing is expected to change. Israel’s peace treaty with Egypt will remain in place and IDF relations with the Egyptian military – particularly vis-à-vis Sinai – will also continue.What consoles Israel for now is that Mohamed Morsy – Egypt’s president elect – will have far greater challenges to deal with than to pick a fight with the Jewish state.Could it be that the Egyptian generals know something about the Muslim Brotherhood that Israel doesn’t? Since Mubarak’s downfall, Israel has been quietly preparing for a possible conflict with Egypt. Not one that will happen tomorrow or even next year but sometime in the coming decade.The reason that the preparations needed to begin already now was because for the past 30 years the IDF has lived in something of a state of luxury, focused just on the northern front and the occasional faraway threat like Iraq or Iran. Now, it needs to begin considering its southern front again as well.When Lt.-Gen. Benny Gantz took up his post last February, he was presented with two plans. One called for the immediate establishment of new divisions, the procurement of new fighter squadrons and the bolstering of the navy to counter a potential future threat from Egypt.The other plan, which Gantz selected, was more cautious and was done with the understanding that even if the Muslim Brotherhood takes over it will still take some time before Egypt threatens Israel again like it did in the days leading up to the Yom Kippur War in 1973.For that reason, the past year has been spent within the Southern Command mostly learning about Egypt and preparing conceptually for the future.It is one thing if there will be a war, but Israel is actually more concerned with the middle-of-the-road change and how to respond. What happens, for example, if in a year from now Morsy gives the military an order to move a division to the Sinai Peninsula for training. This would be in violation of the peace treaty, but would Israel go to war in such a case? Probably not.Morsy’s victory will also hinder Israel’s operational freedom the next time there is a flare up with Hamas or Islamic Jihad since air strikes in Gaza will quickly lead to a crisis with Cairo.Here is another question – what does a Muslim Brotherhood takeover in Egypt mean for a potential Israeli strike against Iran’s nuclear facilities? Does Israel need to be concerned now about potential retaliation from Egypt or not? If so, then does this mean that Israeli attack plans have been moved once again to the backburner? Or maybe one has nothing to do with the other?Egypt’s economic state has been in decline since the toppling of Mubarak last year.Investors have fled the country and fiscal deficit has ballooned.Israel is actually hoping that due to the dire economic situation, Egypt will remain dependent on other countries for assistance, particularly the United States and Europe. That assistance, Israel hopes, will serve as some leverage in ensuring that Egypt retains normalized ties.The question that bothers Israel is what will happen several months or a year from now after Morsy settles in to the presidential palace in Cairo. The IDF’s concerns range. Firstly there is concern of how the Muslim Brotherhood’s victory will affect the growing terror threat in Sinai and whether Morsy will take action or leave the situation as is.On a larger scale, no one in the defense establishment is really talking about the possibility of a war with Egypt but the Egyptian military council’s decision last week to deprive the president of some of his rights, notably the right to go to war, raised an eyebrow or two at the Defense Ministry.