Based on various blogs and news reports:

UP (SP) Shasta line - there was flooding in Dunsmuir, but I never saw anything specific to the railroad being closed for any reason.

BNSF (WP) Hiline - flooding reported, but point is moot as there is nowhere to go. There may be some trains tied down on the line around Almanor and other places.

UP (WP) - flooding reported around Portola and Quincy, unknown how it affected railroad. Feather River Canyon is presumably out of service - likely due to slides and washouts. Probably won't know the extent until flooding recedes and they can get in there to asses presumed damage. Hiway 70 currently showing closed from Jarbo Gap to Greeneville Wye/Jct CA89, so any survey may have to be by air.

UP (SP) at Elk Grove - derailment. May be due to washout. I haven't seen any estimate as to cleanup and repair.

UP (SP) over Donner - intermittent closures due to flooding, slides and avalanches. It does sound like there are bigger problems in Northern Nevada. East end of Elko yard was flooding as well as low lying parts of town. A few days ago a small dam broke in the Wells/Montello area supposedly washing out hte former SP. Extent of damage not known, may or may not reopen quickly?

UP already reported detouring their and BNSF trains over the old LA&SL - Salt Lake/Ogden through Vegas to Barstow, then over Tehachapi. Someone posted the last Salad Shooter was still trying to take the Overland route and already lost a day. Amtrak turning the Zephyrs back at Salt Lake City.

For BNSF you also have to consider their issues in Washington - Marias Pass (GN Hiline) intermittently closed due to avalanches. MRL (BN/NP) only has limited capacity and I imagine trains are backed up already. Unless UP is detouring the Inside Gateway trains down the old SP, how is BNSF getting that traffic moved? I think Kelso-Chehalis still closed to occupied passenger trains another day due to concerns about possible slides, but I believe freights are still running. BNSF had service issues due to congestion and weather before this round of route closures.

I haven't heard of any major issues with the Cascade line. I've heard trains running through town, so evidently the UP line from Hinkle through Idaho and east is still open without issue. Weather here has turned sharply from hard winter to a warm like spring with lots of snow and ice melting due to temperatures and rain, and there are issues with slides/avalanches and flooding but nothing I have heard adversely affecting the railroads lately.