Agilent interlocks should be reset
Interlocks on the SL C100 modules being warmed up should be increased to match those on 2L07 (fig. 3) so the relief plates don't lift if there's lots of frozen air within. Since 2L26 is being pulled that system might simply be turned off, perhaps first turning off the turbo and then opening the right angle valve so the scroll pump can bring the vacuum back down to the mTorr range. Then turn it off too.