Confusion regarding re-entry permit and work visa process

On October from last year I went to Japan on a w hv (valid for 12 months). I stayed two months and then went back to my country (Spain). At the time of leaving:

1) I did not unregister my address in Japan given that I intended to come back a few weeks later

2) I filled in a form for a special re-entry permit in the airport, which they've put on my passport

After that, and for personal reasons, I was not able to come back to Japan. During all this year I've not held any job and have not had any income whatsoever, not in Japan, not in Spain.

Fast forward to today I'm still in Spain, however, I've signed a contract to work Japan, and I obtained the CoE very recently. A couple of days ago I've submitted my visa request in Spain, submitting my CoE, passport etc. I worry now that they might deny my visa due to still holding a valid visa and the zariyu card associated to it (still valid), as well as a re-entry permit. I did see in one of their websites that being a visa holder or holding a re-entry permit may be a reason for work visa denial.

Should I expect any complications from this?

by a-lawliet