Visa problems

Hello everyone. I'm hoping very much that there is someone out there who had the same problem as I have now. And maybe can help me out!!
I'll try to explain everything clearly, but if there is something not clear, just ask!!

Ok there I go...

I'm going to Japan from October with a studentvisa for one year, because i'll be studying at a Japanese University. My date of issue is August 22 and date of expire is November 22. It is kind of long stay resident in Japan-visum.

But, the problem is, I'm also going to Japan in September, from 9 untill 22. Just as a holiday. Means I wasn't planning to use my Visa. Only showing my passpord and get a stamp. But my visa is in my passport, and they will figure out my visa and stamp off my visa. And so I will not be able to re-entry Japan again in October. I really don't know what to do now! (And i don't have the time in Japan between 9 and 22 October to get a re-entry-permit.)

Hope there's someone out there who can help me!!!
Yoroshiku!!!!

Have you asked the Japanese Embassy/ Consulate in your area about this? They are the first people to ask about any visa issues, and can give you the most accurate information.