It’s been a while since I’ve used @pause in Repetier (For 3D filament changes), The behavior should be: @pause encountered in code, Pause message appears on screen with button to resume, and on press, the gcode program picks up on the next line. If Repetier does pause for you on an M00 (I don’t know why mine did not) than the above might work for you. I need to try both @pause and M00 in repetier and see if I missed something before. Perhaps there’s a G/M code to restart from the terminal/console.
These Repetier Host commands look useful, especially @isathome – Sets the current X, Y and Z coords to Zero’s.