Yes The phrase is grammatically correct and sounds natural. It clearly conveys the idea that you and your friend have resolved your differences after a significant time apart.
You could also say :
1. "My friend and I reconciled after a long period of conflict."**
2. "After a lengthy disagreement, my friend and I found common ground."
3. "My friend and I buried the hatchet after a long time of disagreement."
4. "After a protracted disagreement, my friend and I made amends."
5. "My friend and I restored our friendship after a long disagreement."