Account not deleting messages

I use a local program. I archived 2500 of my 3,000 sent messages to another folder in my local program. The sent folder syncs. Things I send quickly appear in webmail. However, instead of having 500 messages in sent as is on the local computer, I have 3000 still in webmail. Waited a day, still there. Tried the index sync thing. Still there. There are only 500 in the local folder. This is the automatic Sent folder beneath the inbox.

When I archive from other folders, it seems to work.

I am logging in with my domain email and using an alias to filter my emails with that domain name to a folder. Is that an issue? Will I need to delete the messages by hand in webmail?

What I’d like to do is reduce total storage.