All is not lost. I'll bet galvenize doesn't know about the nature of the true ending. I played VLR first. I would not recommend doing this, but it didn't blunt the impact of either game as much as people might think. Though admittedly my own fuzziness over the ending of VLR helped to preserve many of the twists in 999. If I had went out my way to figure out the end of VLR (e.g., using the official FAQ or reading spoiler threads), it would have certainly blunted 999's impact. Fortunately, I was foggy enough that not only was I still shocked by everything in 999, but it made me understand and appreciate the true nature of a few characters in VLR.
After I finished 999, I looked up everything and my mind was blown. Of course, it would have been better doing it the other way around (especially considering how much of a chore the gameplay can be sometimes in 999 compared to VLR), but I was still able to fully enjoy both games playing them out of sequence.
There is one advantage to playing VLR first. You're not disappointed by it lacking the great 2D art of 999.