I take it you have sync off on the phone, otherwise the changes and deletions would have synced to your account as you made them and all would be good. That's what you should have done when editing on the phone. Now, when you enable sync there's some chance that all will still be OK. But, if you made major changes you may get an error message, something about too many deletions or similar, and sync will fail. This is actually a kinda fail-safe system to keep users from accidentally deleting all their contacts.
You can export contacts on the phone as a .vcf file (do this as a backup *before* attempting to re-sync as above), delete all contacts in the account, then reload them from the .vcf file.
In the future, the best method for doing major revisions to contacts is to disable sync on the phone, edit contacts on the computer, export as .vcf for backup, delete all contacts on the phone, then re-enable sync to download the revised contacts list.