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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Intel Integrator Toolkit (ITK) takes, as input, a BIOS package (a .BIO file). It then presents you with various scenes that allow you to customize various portions of the BIOS and firmware. This include BIOS configuration parameters, SMBIOS strings, Splash Screens, etc. and etc. Once you have made all of the customizations that you would like, you save these changes into a new .BIO file. This .BIO file can be installed just like any other .BIO file (in fact, the ITK tool can even generate an Express BIOS Update executable for initiating the install of the BIOS package from within Windows); the only difference from the original .BIO file is that, by default, during the installation process and because of the customizations included, the user will be asked for permission to install the customizations.
That's it in a nutshell...
P.S. I would also note that, once customizations are installed, they will stay in place unless a subsequent .BIO file overrides them or, in the case of BIOS configuration parameters, these are changed from within BIOS Setup (Visual BIOS).