Leaving Japan after contract is up - Visa

I have a question that I haven't been able to find a solid answer to on the internet. I'll explain my situation first.

I'm currently on a one year work visa as an English instructor. It is valid until August, but my contract ends in late March and I won't be renewing. Before I return to Canada, I'd like to travel to Thailand/Cambodia for a month. I intend to:

1) inform immigration and complete the "moving/leaving" process when my contract is up
2) head to SE Asia early April (from Narita)
3) return to Japan early May (to Haneda)
4) return to Canada after a day or so in Tokyo to collect my luggage. Upon this final departure from Narita I'll hand in my residence card.

I'm wondering if I can travel to SE Asia and back without forfeiting my Japanese residence card. My last paycheck will be paid at the end of April, and if I don't have residency at that point, the taxes on my last two paychecks increase from ~2% (Kou income tax) to 20.42% for a non-resident. I'm worried that I'll lose my resident card going through immigration at Narita and have to return as a tourist to collect my luggage (I'm Canadian so it'd be free). If that's the case I'm out close to 100,000 yen. I'd like to avoid that if possible.

Sorry if this isn't clear. I've emailed my employer to clarify with some of this but I haven't heard back. If anyone can help that would be great!

That should be no problem; even after you cease your activity, you can still leave Japan on the "special re-entry permit" system as long as you have not received a notification that your status is up for revocation, and this cannot happen sooner than three months.