SANTA CRUZ COUNTY (CBS SF) — As the atmospheric river continued to pound the Bay Area with rain Wednesday night, evacuated residents who were forced to leave their homes in the Santa Cruz Mountains earlier this week are still being warned to stay away.

The potent atmospheric river that had stalled off the Monterey County coastline Wednesday morning edged back north by early afternoon, triggering new flash flood warnings in San Mateo and Santa Cruz counties.

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Thousands of residents were told to evacuate from their homes in the Santa Cruz Mountains in the CZU Lightning Fire burn zone in advance of the storm, but the fury at least of the first thrust of the system did not generate the of the feared mudslides.

While the Flash Flood Warning that was issued for the CZU Fire burn scar expired at 6:30 p.m., a Flash Flood Watch would remain in effect until Thursday afternoon in that area of Santa Cruz and San Mateo counties as well as other parts of the North Bay and Monterey County.

KPIX 5 Weather Center: Current Conditions, Maps, Forecasts For Your Area

By Wednesday evening, Boulder Creek in the Santa Cruz Mountains had received nearly 4.5 inches of rain, with Saratoga picking up 2.85 inches, Morgan Hill seeing nearly 3.25 inches and Ross receiving 2.42 inches.

In the East Bay, Dublin got 1.34 inches, while both San Francisco and San Jose received less than an inch of rain with .91 inches and .81 inches, respectively.

Early Wednesday afternoon in Santa Cruz County, Cal Fire extended an evacuation order through the evening given the additional showers forecast into Thursday morning that are expected to meet or exceed thresholds for debris flow. The evacuation orders in the areas of San Mateo County endangered by the fire burn scar were also extended.

“We understand that people are probably starting to get frustrated, especially now that there has been some lulls in the storm,” Battalion Chief Nate Armstrong with Cal Fire told KPIX 5 Wednesday night, but still urged evacuees to stay away until orders are lifted.

“We had isolated flooding, isolated small mud slides, rock slides. It’s a very small scale, but it’s definitely an indicator that the potential is still there,” Armstrong went on to say.

The evacuations are largely in areas in or near burn scars from last August’s CZU Lightning Complex fires, with more than 5,000 people estimated to be affected in jurisdictions of the Ben Lomond, Boulder Creek and Felton fire protection districts and the Santa Cruz County Fire Department. People can find out if they are in an evacuation zone by visiting the community ZoneHaven website.

The Boulder Creek Fire Department monitored the storm through the overnight hours. By dawn on Wednesday, it looked like they had been spared; the storm’s track has shifted southward, lessening the threat of mudslides. But by midday, the rain came roaring back.

“I would ask you — urge you — to please re-consider the decision to leave. The weather is unpredictable. On the fire side, we react to whatever comes down. We try to prepare as best we can. If we’re told that there’s going to be an impending storm, we gear up and get ready for it,” says Chief Mark Bingham.

Chief Bingham says the department is in disaster response mode and will not resume door-to-door evacuation orders. The second wave of rain is keeping crews in the Santa Cruz Mountains on high alert.

“Most of the houses in my area are still there. But there are some above us that aren’t — that burned,” said homeowner Gregg Schlaman. He chose to stay at his Boulder Creek home, ignoring evacuation orders.

He spent much of Wednesday checking on the damage in his community. And as the storm returned, he took to social media urging evacuated neighbors to think twice before returning.

“There’s people who want to come home right now. And as someone who’s very vocal on social media in the community, I’m trying to keep people aware of what’s going on,” Schlaman said.

Three temporary evacuation point shelters were set up around the county for evacuees, but two closed as of 1 p.m. Wednesday. The location at San Lorenzo Valley High School at 7105 state Highway 9 will remain open, but sites at the Scotts Valley Community Center and Pacific Elementary School are now closed.

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A call center has also been set up at (831) 454-2181, and a map of county road closures can be found online.

A Flash Flood Watch was in effect for all burn scar areas across the Bay Area through Thursday afternoon. The weather service also said an Urban and Small Stream Flood Advisory was in effect until 5:15 p.m. Wednesday in poor drainage ares of southeastern Alameda County, southeastern San Mateo County, Santa Clara County and Santa Cruz County, as well as parts of Monterey and San Benito County.

The weather service said cities that could see flooding include San Jose, Fremont, Sunnyvale, Santa Clara, Redwood City, Mountain View, Milpitas, Palo Alto, Santa Cruz, Cupertino, Watsonville, Gilroy, Newark, Campbell, Morgan Hill, Hollister, Menlo Park, Saratoga, Los Gatos and Los Altos.

PG&E was reporting approximately 16,200 customers without power as of Wednesday evening. The outages were concentrated in the South Bay (8,120) and the North Bay (5,023) with an additional 2,331 customers without power in the East Bay. Only 400 customers in San Francisco and 326 customers on teh Peninsula were effected.

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The atmospheric river roared through the San Francisco Bay Area early Wednesday, flooding roadways and downing trees and power lines with substantial rains and high winds.

Across the Bay Area, the heavy downpours caused minor flooding on local freeways, downed trees and knocked out power to at least 36,000 homes. Winds were clocked as high as 80 mph on Mt. Diablo in the East Bay and 84 mph in the Santa Cruz Mountains.

In Rohnert Park, powerful overnight winds sent a 100-foot popular tree crashing into a trailer at the mobile home park around 9 p.m. At the time, the two residents were home and narrowly escaped a tragedy.

A woman who lived in the trailer was in bed when the tree crashed through the ceiling, ending up just a few feet from crushing her.

Meanwhile in Marin County, the strong winds and rain brought a large tree crashing down on top of a car in Inverness. The Marin County Sheriff’s Department said it happened around 9 p.m. Fortunately, no one was injured, according to authorities.

The winds also jack-knifed a big rig accident on the Bay Bridge, causing serious traffic delays Tuesday night.

Three lanes were blocked on the Bay Bridge in the eastbound direction at the Treasure Island off-ramp. Wind was cited as the cause of the truck being pushed to the side around 9:45 p.m. The CHP cancelled the sig alert at 11:28 p.m. and the big-rig was off the bridge at 11:35.

The plunging temperatures also brought snow to the higher elevations in both Lake County and in Santa Cruz County.

The snow reached as far north as Dublin, where California Highway Patrol officers shared pics of a snow-covered roads in an unincorporated area of Alameda County.

While the steady heavy rain continued to pound the Big Sur coastline, forecasters said the Bay Area will experience intermittent downpours and thundershowers for the remainder of Wednesday.

“For much of the populated areas numerous showers and isolated t-storms will continue on and off today through Thursday with cool daytime highs in the low and mid 50s,” the weather service said.

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The storm threat also impacted the COVID-19 vaccine roll out in San Francisco. Citing the threat of high winds and heavy rain, city officials shut down the City College vaccine site until Friday morning.