Good grief.

Most of us use an email client precisely to avoid having anything to with webmail, and here you are voluntarily and deliberately using both, so you have the worst of both worlds.

Why bother with Thunderbird if you're prepared to use webmail?

However, how is the account configured in Thunderbird? POP or IMAP? Who is the email provider? Outlook/hotmail/live currently has some very odd quirks when connected via POP.

Habit I guess from my early days. Just found it easier to use the webmail offered by my provider, a Local phone company, to go through all my emails and get rid of what i didn't want on my computer/in my inbox. Before I used Netscape to download them and go from there. Save a lot of space and worry about bad stuff showing up. (horror stories about opening an email let alone an attachment and getting bad stuff on the puter). Been through several computers and all the windows versions and Thunderbird since it came out, and never had the emails I wanted to stay in my inbox disappear, or setup changing. Checked with the provider, they say either is usable, so left in Thunderbird's default IMAP. Don't know whose software the mail program is, but a program called Baracuda intercepts some mail it doesn't like and shows up in my inbox asking what to do with it.

I suspect you are accustomed to using POP but have now set up to use IMAP. Check with your provider for their POP settings and make a note of these.

Go to File|New|Existing Mail Account, add the account again. If it doesn't offer POP, decline the offered IMAP settings, select Manual Config and enter the POP settings. Once it's working, you can remove the IMAP version. Select it, go to Tools|Account Settings, click the button at the bottom of the pane and select Remove Account.

I can't see why your tortuous webmail/email procedure shouldn't work with IMAP, but I think you have got used to clearing the server and that just isn't how IMAP works. If you delete a message in the server, it will vanish from the account in the client too, and vice versa.

I don't know that I have ever got an infection via email when using Thunderbird. You have to explicitly open and run an attachment for it to do any harm, (at which point the real-time scanning function of your AV should intervene) and I don't understand your bad experiences. In Thunderbird, normal scripting within email messages is disabled by default (and by design) and checking that links go to where they say they go to is a valuable precaution. Usually you can just hover over a link, and Thunderbird's status bar will show you its true destination.

You can use an IMAP-connected account in a way that mimics POP; just move all messages that you want to keep to the Local Folders account. (This moving can be automated by a Message Filter.) Doing this will download the messages, make a local copy and remove the server copy.

I move messages that I want to keep into appropriate subfolders. This means that after my filters have run and have moved expected messages into their own folders, what is left in the Inbox is unexpected and usually treated immediately as Trash or Junk. So I don't have to do much "weeding" in the Inbox. Similarly, I move sent copies into the same subfolders, so the complete to-and-fro conversation is kept together in the proper folder and like my Inboxes, my Sent folders should only contain odds and ends that had no immediately obvious home.

So, in my own way, I am keeping the Inbox clear in my accounts, whilst using IMAP to deliberately make useful messages and conversations visible to all of my computers, my tablet and my phone.

thanks for the help. Switched to POP, everything seems to be "back to normal". Looks like I have a few habits to relearn. And a lot to learn about a program I thought I knew enough to get around in! Looks like my provider trying to help just left me confused.