I currently have and use a number of emails in my workspace (all with the same domain, annual subscription for IMAP). Recently, I used one of those emails and set it up with an office 365 email account. Everything is working ok with it.
However, last night I began encountering problems with my other email inboxes in workspace (such as email@example.com and firstname.lastname@example.org) - thinking that Microsoft had took complete control over my email's DNS settings for my domain.
Then this afternoon, I noticed that the email inboxes I have set up in my Workspace Emails are working fine now.
Can this set up continue with no problems?
PS - I purchased the office 365 licence from Microsoft, rather than via GoDaddy, if that makes any difference?
You cannot use Office 365 and our webmail with the same domain. They both have different MX records, having both set of records, will cause intermittent issues with all email accounts. You either will have to remove the Office 365 records and continue to just use webmail or vice versa.