Yes, when you re-upload a PGN file (with the same games), it will skip already existing games (in that database). A game is considered a duplicate if the following is true:

1. You played the same pieces (white/black).
2. The date is the same.
3. Name of your opponent is the same.
4. The position reached after 40 moves (or at the end of the game if reached earlier) is the same.

In case, all four criteria match, we skip the game as we believe it is already present in the databaase.

However, please note that you can have duplicate games across multiple databases.