Flags set in Mac Mail being reset on sync to Exchange

Hi everyone
A couple of my Mac Mail accounts sync with an Exchange server at work. So far so good, but I use flags extensively in Mail as part of a GTD approach to time and task management: Urgent, Not Urgent, Some Day, Awaiting Response, Delegated and Done.
Only problem is that these flags keep getting reset to Red every time Mac Mail syncs with Exchange, though oddly enough Exchange seems to leave them alone if I've set a flag whilst not connected to my work LAN.
So typically I flag an email as Done, but come back 5 mins later find that it's been reset to the red flag in Mail which I reserve for Urgent. This definitely doesn't help GTD
Before anyone asks Ive gone into Exchange and tried to duplicate the flag structure and names, although I had a feeling this wouldn't work: and it doesn't.
I've tried looking this problem up online as there must be many users of Mail who sync their inbox with an Exchange server and who also use flags to tag messages, but without finding a way forward.
Any thoughts would be much appreciated.
Thanks, Tom

If the other folders you're referring to are local folders to the PC, they will not be available to any other devices no matter what mail application you are using.
If you check the sidebar in Mail at the bottom, any other folders on the server will appear under the Exchange account name. Expand the folder to see what's there. If the other folder are on the server, they should appear there.

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