You may be experiencing an issue similar to the one described in the following article, i.e. Thunderbird may be using the wrong profile, in which case you may solve the problem by telling Thunderbird to use the right one:

https://support.mozilla.org/kb/recover-user-data-missing-after-thunderbird-update

yes I have gone through those steps to try and fix the problem but no luck. any more ideas?

When you say you've already tried that, you mean you've tried launching the other profiles and the missing data doesn't appear in any of them?

If you open the profile folder in the file manager of the OS you're using, then go one level up to the enclosing Profiles folder, do you see additional profile folders there that might not be available in Thunderbird? The mail folders you miss in Thunderbird must be in the Mail folder of one of those profile folders…