I recently changed computers and copied my old email inbox into my new profile.

This doesn't sound right. What exactly did you do?

I will try to clarify:

I was on Linux Mint 16 and my system crashed. After I rebuilt my system, I restored my email by copying an older <profile>.default folder into /home/<username>/.thunderbird. I now had two folders under /home/<username>/.thunderbird and for reference I will call them <profile-new>.default and <profile-restored>.default.

This is when I first noticed that I could not use the delete button nor the right click menu option to delete emails for anything in the <profile-new>.default profile.

Soon after that I migrated to xubuntu 14.04, using Thunderbird 24.5 and copied both <profile-new>.default and <profile-restored>.default folders and the profiles.ini file into my /home/<username>/.thunderbird folder. I did this prior to starting Thunderbird so that when I started Thunderbird for the first time, it found the profiles.ini and used what was already in the folder instead of making me build a new profile.

However, I still could not use the delete button nor the right click delete option on any email in the <profile-new>.default profile. If you look at the screenshot below, these are all the emails in the folders on top. Any emails in the Local Folders on the bottom, I can delete using the delete button and/or the right-click delete option.

Also, you can see that there is a closed lock overlaid on the envelope next to the top profile.

So my question is this: what permission/setting is set that prevents me from deleting those emails? And how do I fix it?

permissions on both folders and subfolders are drwxrwxr-x and files all seem to be -rw-rw-r-- and all are owned by me.

Thanks.

Padlocks simply indicate accounts that use secured connections, with TLS or SSL.

I don't understand what you were trying to achieve by copying the old profile in; profiles are mutually exclusive and you can access only one at a time within a single instance of Thunderbird. You generally have to jump through hoops to use multiple profiles.

I get the impression that you've actually copied bits of one profile over another, and I have no experience of what happens when you do that. To blend bits of different profiles together, I'd import mailbox files using

https://addons.mozilla.org/en-US/thunderbird/addon/importexporttools/ 

but I would also recognize that these are mail stores and not working accounts, so would necessarily import into Local Folders (since imported messages don't intrinsically "belong" to any specific email account.) You can of course drag-and-drop into the preferred account folders after the fact.

The prefs.js file actually stores the details for working accounts, and if this isn't consistent with copied-in account folders then it's possible that Thunderbird doesn't "know" where to find things.

Thunderbird's profiles system doesn't lend itself to merging. :-(

You can trivially set up an entirely new profile, or less trivially, insert a complete old profile in place of a new one. Combining two or more is usually painful.

Incidentally, I'm using LMDE here, but have always taken care to transplant entire profiles and have never experienced the inabilty to delete. Having said that, the inabilty to delete messages in Thunderbird is one of those regular complaints that pops up here every now and then. It seems to affect all platforms, so I don't think you being on Linux is of any particular relevance.

<profile-new>.default and <profile-restored>.default

How do you start Thunderbird, and with which profile?

Have you tried to rebuild the index file of the troubled folders?

Right-click the folder - Properties - Repair Folder

I did the repair folder, but I still can't delete.

Thanks for all the info. I've moved the email from the profile-new to profile-restored and I will point my downloads to that profile.

Thanks again.

When did you compact folders the last time?

I will point my downloads to that profile.

I don't think I understand what that means.