Apple Mail Disappears from Folders

I am very organized. When I finish reading an incoming email I drag it to a folder dealing with that subject. Some of the folders are empty when I return a few weeks or months later - (my original message had the wrong OS listed... It should be listed as  Mavericks 10.9.5).

Bill
Many thanks for the kind reply. I finally installed Thunderbird and so far everything is good.  Time Machine  would, were I using the laptop in a more traditional setting, help resolve this issue. However I am prepping for a year + back pack trip to South America and elsewhere and the MacBook Pro is going along.  What I have done is install Time Machine Editor (since Time Machine is parsimonious about daily updates) and update now once a week. Better than nothing and given what my schedule on the road may be like its a better fit than once a day. One would think Apple would make Time Machine  more controllable particularly in the versions of OSX that are installed in laptops.....
In any case this is my first MacBook Pro and my first Apple computer but I am a long time Linux/Unix user so feel right at home with OSX. In spite of the mail problem, this is without a doubt  the best laptop I ve ever used....and I ve been using them since they were suitcases
Regards and many thanks for the kind read and reply.
Carr

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