question about Japanese tourist visa:

if I enter on the 30th March, then I'll get a visa stamp on my passport on the 28th June (90 days).

if during this period, I exit Japan, say 15th April, and enter 30th April, will I get a new visa stamp 30th April + 90days?
Or they will continue from that old visa stamp?

for IC cards, if the balance is less than the handling fee, there's no charge right?

say if the IC card got 10 yen left, when I return it, I can get ¥500 plus ¥10 = ¥510?