This is a common problem with SharePoint online and Office 365, like all other Office apps SPD has the option to sign in with a live or corporate account and this will save some of your settings.
SharePoint Designer
If you are using your corporate account in SPD and a different live account on Windows is possible that after installing a Windows update your corporate account on SPD will be replaced by the Windows account.
This message will be also displayed if you manually switch accounts.
To continue to open your SharePoint online site do the following:
On SPD go to File Account
Click on Switch Account
Sign in with your corporate account
Open your SharePoint site
Unable to check in file
…the file is no longer checked out…
This is another common issue and it is caused by the settings that are save in the SPD cache. Unfortunately, this issue only goes way after cleaning SPD cache and this procedure will wipe all your sites history.
How to clear SPD cache
Make sure SPD is closed
On your keyboard press + R
Open SPD folder
Paste the path bellow in the text box
%USERPROFILE%\AppData\Local\Microsoft\WebsiteCache
Delete everything in the folder
On your keyboard press + R again
Paste the path bellow in the text box
%APPDATA%\Microsoft\Web Server Extensions\Cache
Delete everything in the folder
Open SharePoint Designer
Go to File Options General
SPD Options
Click on Application Options
On the General tab uncheck Cache site data across SharePoint Designer sessions
SPD cache
After clearing the cache, you will be able to check in your file using SPD.
Unable to see list and libraries on SPD
This happens because you have a corrupted list in your site or because you have a list that was deployed by a feature that no longer exist.
Open SPD Lists
To fix this you will need to delete the corrupted list, if you don’t know what is the list causing the list you will need to open the lists in your site one by one until you find the typical error message Something went wrong.
After deleting all faulty list instances refresh your SPD.
