Compacting shouldn't remove messages that you have kept. Compacting only removes old messages that have been marked as deleted. More about Compacting: https://support.mozilla.org/en-US/kb/compacting-folders It is recommended that you SHOULD do this every now and then - so you shouldn't have to come here going "Uh-Oh."

There are a few things you could try. Let us try repairing that folder ... In the Folders Pane on the Left find the local folder with the missing messages. Right Click on the Icon of that folder (still in the Folders Pane on the Left) and Choose Properties. Click the Repair Folder button then Click OK. (Wait a while for repairs to finish ... ) Look again to see if any messages have returned.

I've tried repair folder. It's no use. I use my webmail with thunderbird. Now I can't find those mails in my server website.

I conclude that sometime in the past those messages were (I presume accidentally) flagged for deletion on your server side. And the Compacting them did the job of removing those messages that were so flagged. If you had made a backup of your Profile Folder at some time in the past ... https://support.mozilla.org/en-US/kb/profiles-where-thunderbird-stores-user-data ... you might find that those messages still exist in the backup. (You might want to backup what messages you still have left, now?)

I am new here and I'm sorry I couldn't be of more help. I hope one of the other support volunteers has better suggestions.

> I conclude that sometime in the past those messages were (I presume accidentally) flagged for deletion on your server side.

This can't have happened if this is an imap account, because your original assessment is correct [1]. (assuming Thunderbird was actively syncing all this time)

[1] Compacting shouldn't remove messages that you have kept. Compacting only removes old messages that have been marked as deleted. [and those deleted messages would have no longer been visible in THunderbird, unless you had "mark as deleted" enabled]