Where did the emails in my inbox go

This happened before but I’m more aware of what is happening now.  All the previous emails in my inbox disappeared after I downloaded and installed another program on my computer.
I’m using Windows 10 and eM Client for my Hotmail account.  The eM Client set up the account automatically as a IMAP account. Even though eM client set up the same account as a POP3 account when I log on as a different user.  This disappearing email only seems to happen in the IMAP account and there is no option in the IMAP setup to purge the emails from the server.  Is there a fix or should I try to configure the Hotmail account as a POP3 account using the “other” service link in the eM Client account setup.

POP protocol downloads your messages locally from the server and then DELETES them from the server.If there are any messages on the server, POP will view them as new and download them.
IMAP doesnt download your messages and always synchronizes to your server. If you deleted the messages from the server by checking your email with the POP account previously, there is nothing that the IMAP account can synchronize to.
If you want to access your mail from more places, I suggest setting all your accounts as IMAP. But do not do this before saving your messages from the account where you have set it up as pop, as removing it now and changing to IMAP would delete all your messages that are stored locally.
I suggest exporting your emails that are saved locally using the File>Export> Export emails to .eml option and then removing your account and adding it again manually as IMAP. Then use the File>Import to import your messages back in. Adding them in eM Client will synchronize the messages back to the server as well.
If you do not want to lose any data, make sure you backup your database with the POP accounts before you start readding your accounts.
Hope this was helpful, if you experience any more trouble, dont hesitate to ask again.