Can money taken from an employer be considered compensation for lost money, and will the person who did that remain under Allah's shade on the Day of Judgment?

The greatest injustice is to consume people's wealth unlawfully. If you have taken money without a rightful claim, you must repent to Allah. Part of perfect repentance is returning the money to its owner, even if indirectly. The Hadith: "Whoever prays to Allah for forty days in congregation, catching the first takbir, will be granted two immunities: immunity from Hellfire and immunity from hypocrisy," relates to catching the first takbir for all prayers, not just Fajr prayer. This righteous deed prevents its doer from engaging in the deeds of the people of Hellfire and hypocrisy. If it is established that money was taken from you unjustly, and you can reclaim it through legitimate means, then do so. If you cannot, and you come across some of the unjust person's wealth, you may take from it an amount equivalent to your right.