Multiple Apple ID accounts – can I delete one safely? I have two Apple ID accounts and wish to remove one as it causes confusion with password issues. What problems will this cause if I delete this app from my iPhone.
The main issue you might have is if you have purchased/downloaded apps, music or any content with that apple ID. You won't be able to update them or you will need to re-download them or purchase them again with the other ID in order to continue having updates.

The same applies with synced content via iCloud such as contacts, iCal, etc.

You just need to be sure that no content, apps or anything was synced or downloaded with that ID.