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The "drive not ejected properly" could be one of several points:
- the USB driver chipset
- the power supply to the USB port
- the USB connection on the computer
- the USB cable
- the drive housing
- the drive itself is failing
- the drive has gone into a power-saving / sleep mode
It's a few places to try and troubleshoot, but as you say, having some tracks on reserve on the internal drive is always a good fall-back.
You can migrate the files to your internal drive without issue, simply move the files, then relocate them all. If you keep the same folder structure as you use on the external, the relocation process will be fast and allow you to batch-relocate with just a few clicks. All of the track data will be retained.
If you have the database on the external, I would recommend moving it to the internal, which would allow you to use the music from the internal drive even without the external drive connected.