A colleague helped me resolve the issue. I had to hover my mouse over the RStudio icon on the taskbar until the preview popped up. When I moved up to hover over that I was able to right click and select maximize which brought the window back.
I don't really understand what happened because if it was simply the case that the window was minimized, then win+arrows, cascade windows, or tile windows should have brought it back. It also doesn't explain why when, for example, I selected cascade windows that it "skipped" a step and acted like a phantom window was there, or when I had two windows open (chrome + RStudio) and selcted "show side by side" it put chrome on the left half and the right half showed the desktop.
Regardless, multiple people have clearly had the same problem so I wanted to be sure to post my answer for others having the same problem in the future. I felt like I was in xkcd 979, so now hopefully the next person won't feel the same way.