If you enter a portal and use Hourglass the map gets deleted and Hourglass acts as if it didn't get any uses upon entering a new floor, meaning if you had 2 uses on the previous floor and you enter a portal on the next and use Hourgalss you are left with 1 use.
Streamer ran into this today, I did some testing. It's even worse, it actually deducts an extra charge every floor. So 3 floors in, using glowing hourglass after taking a portal completely empties the item.
If you enter a portal and use Hourglass the map gets deleted and Hourglass acts as if it didn't get any uses upon entering a new floor, meaning if you had 2 uses on the previous floor and you enter a portal on the next and use Hourgalss you are left with 1 use.