Why does LPX sometimes shorten, cut,

All, does anyone know why, maddeningly, Logic Pro X sometimes cuts, shortens, and/or converts to 8 bit audio files that then can't be played back?
This has been happening to some of my audio tracks (24/44.1 files) that I record into Logic, but it only shows up after I save the project file to my external SSD Thunderbolt drive then re-open to work on it the next day.
Is it possible I'm somehow saving the project incorrectly? To a wrong disc? When saving I check the "organize into a package" and the "save audio files" options in the save as window.
I usually use the "save as" function, but have sometimes used "save". Does it matter? I've always set up and run my DAW this way with no problems until just recently. I have done the Yosemite upgrade because it looked as though people liked it and there were no problems.
I run OS Yosemite 10.10.1, latest Logic release, a Macbook Pro Retina laptop with 2.7 gb i7 Core Duo and 16 gigs RAM, along with a Focusrite Saffire pro 16 (latest version) interface. I usually just record audio tracks, no MIDI.
Any thoughts? Thanks in advance.

Thanks for answering!
Now, I'm trying to reformat my Thunderbolt external SSD drive but the "can't unmount disk" error window pops up.
Do you happen to know how to erase/reformat from disk utility without the error?
Thanks!

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