I recently went through this month long saga of switching our office email system from Bell Microsoft Hosted Exchange to Office 365 Exchange Online. This was because Bell was shutting down their system and pushing everyone to Microsoft which you could conveniently buy through them. I couldn't handle that thought so we went to Microsoft directly. This is a warning.
Switching the DNS settings turned out to be relatively easy despite it being the part I was most worried about. Since we use GoDaddy we could use a special app that does the switch for you. There was a bit of a hiccup when it seemed it wasn't switching but it soon became clear that it takes several hours for the change to fully come into effect.
That resolved I started to install Office 365 and the latest version of Outlook on the office computers. I took the exported pst file (all 5.5 GB of it) and imported it into the new Outlook. Then I waited for it to upload and sync to Office Online.
I may have been a bit naive about this working but I figured if it worked on Bell's old system then surely it would work on the new and improved and much touted Office 365. After all they are giving me 50GB of space and Bell was only offering 5GB.
Needless to say I realized very quickly that not everything was syncing and even more worrying emails were not going out and being received consistently. Fairly quickly I switched everyone to use outlook online which seemed to be sending and receiving just fine.
NOTE: The only account that seemed to have issue was the account that is shared among everyone in the office and where all the email gets stored while projects are ongoing. The individual accounts (with less data) were working fine.
So I called up Microsoft and was helped by a some nice people, notably Shane who elevated me to Margo. They ran me through several tests and we had a lot of back and forth trying different things over the course of a month.
Finally in one of my Google searches of frustration I came upon this site. Even though I had asked Microsoft about limits such as this being a problem they had dodged my questions. Now I sent them this link and asked them again: "Is the limit on number of folders really 900?" After a few days they finally confirmed that yes this could be the issue.
Now because of our filing system we had probably 10000 folders so I had some work to do. We redid our filing system and archived many older projects and brought it down to 500 folders. Now the system seems to be working and everyone is somewhat happy.
Apparently the flat, white UI of the new Outlook is annoying to some people....