On most NUC models, SATA Lane 1 is routed to the MSATA/M.2 connector and SATA Lane 0 is routed to the SATA drive bay connector. While you have only a single drive installed, it does not matter which SATA lane is actually being used; you get a single entry in the Boot Order table and it boots from that drive. When both drives are present, however, the BIOS, by default, will list the drive connected to SATA Lane 0 first and the SSD connected to SATA Lane 1 second. In fact, however, you want to (continue to) boot from the SSD and thus you want the order to be the opposite. What you have to do is change the order of the entries in the BIOS Boot Order table so that the entry for the SSD is ahead of the entry for the (other) drive.
It is possible, using the Intel Integrator Toolkit (ITK) software, to produce a customized BIOS Update (.BIO) file that has the boot order set the way you want. Installing this file on every unit will cause the boot order to be changed to these settings. Obviously, you will need to produce one of these customized BIOS Update files for each separate BIOS that you use.
Hope this helps,
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