Messages not deleting from server after being downloaded

I access my emails during the day via IMAP for webmail and on my iPad. When I get home at night, I download the emails onto my laptop via POP3 and they are supposed to disappear from webmail and my iPad. 
They do disappear from my Inbox, but when I file the messages into different folders on my laptop, they don’t disappear from my webmail - they move to the ‘deleted’ folder. They absolutely shouldn’t be there but somehow eM Clients thinks I have deleted them. If I then delete them myself, they disappear from my folders. 

How can I resolve this, please?  

I’m a little confused by your explanation, but maybe an understanding of POP3 will help you.  POP3 downloads messages from a server to your local machine.  It only downloads messages from the server inbox.  There is NO synchronization between the local machine and the server.  Therefore, anything you do on the laptop will NOT be reflected on the server.  There should be a setting in eM Client at menu/tools/accounts/POP3 that allows you to leave a copy on the server or not (note: I’m not a POP3 user, so I can’t lead you directly to the item).

I didn’t quite follow your second paragraph, so If this doesn’t help, please let me know and I will try to assist.

Hi Yasmine.

Yes, when you access emails by POP3 they can disappear from the server Inbox. Depending on the server settings they are either left in the server Inbox as they are, marked as read, or moved to trash. So this is what you are seeing; once you have downloaded to your laptop in the evening, those emails are immediately being moved to trash on the server. This is a normal procedure.

When you file your emails to different folders in eM Client this will not move the messages to trash on the server. That was done immediately when you downloaded them. Depending on your email server, they may be retained in trash for some time, or they may be completely deleted. 

Deleting emails from the server trash folder will in no way affect what is on your POP3 email client. Only deleting them in eM Client can delete them from eM Client. 

If you are not certain that you are using POP3, you can check in the account settings. Go to Menu > Tools > Accounts then by clicking on your account you should see this:

Not this:

Hi Gary, thank you for your reply. I have experimented now and what you say is exactly right. Thank you for resolving the mystery of the messages appearing in my ‘deleted’ webmail folder. They seem to self-delete from there eventually without affecting what’s in my local folders. Thanks again, Yasmine

Hi Jay, thank you for your reply. I think Gary (below) has resolved the issue for me. Thanks anyway for your help.