At 2:30 in the morning on Feb. 3, the police called Michelle Polzine to tell her a car had crashed through the front window of 20th Century Cafe, the Hayes Valley cafe and bakery she owns. Now the San Francisco Planning Department has informed her that when she repaired the expansive windows — at a cost of $15,000 — the subtle changes she made may violate its “historic appropriateness” standards.

The twist? Polzine installed what’s now being labeled an historic facade just four years ago.

In 2012, the San Francisco pastry chef had signed a lease for 198 Gough St. at the corner of Oak Street. The former laundromat was no architectural beauty. Its Gough Street exterior was clad in what Polzine calls “Home Depot tiles” and a high bank of Plexiglass windows, half of which were boarded up.

It took Polzine a little more than a year to turn the space into a working cafe, which opened July 2013. To achieve the vintage-meets-modern decor she wanted, she imported a door from the Midwest and revamped the entryway to conform to the standards of the Americans with Disabilities Act. She also installed what she calls “historically correct hand-glazed tiles made in Pasadena.” Polzine also replaced the grotty windows with two sidewalk-to-ceiling panes separated by an aluminum divider, filling the room with natural light. All these repairs were properly permitted and installed to code, Polzine adds.

In 2014, spurred by eviction attempts, the longtime tenants who lived upstairs applied to the San Francisco Planning Department for historic landmark designation. Cartoonist Rube Goldberg — famous for the fanciful and elaborate contraptions he drew — originally commissioned the building, which was constructed in 1911. Goldberg installed his father in one of the apartments and would stay there when he visited San Francisco.

The city granted the “R.L. Goldberg Building” landmark status. In its December 17, 2014, Case Report, the Planning Department wrote, “The ground floor contains three historic storefronts displaying a remarkable state of preservation, including their original bulkheads, display windows, vestibule paving, doors, and transom.” The cafes and stores on the ground level, they continued, “rank among the best preserved storefronts of their age.” The report was, in fact, referring to Polzine’s renovation.

This seemed like gentle comedy to Polzine, even an achievement she could congratulate herself for, until the accident on Feb. 3. “It was like finding your baby’s face smashed in,” she says. She worked all night to help board up the broken windows so she could open for business.

On Feb. 13, new windows were installed. Her contractor replaced the two panes, along with the aluminum divider whose look she never liked, with three panes of glass and silicon dividers that Polzine planned to gild. Her insurance covered the cost.

Three days later, her landlord called her to report that a neighbor had complained to the city about the change and the city was taking action.

Over the past few weeks, Polzine has been emailing directly with representatives of the City Planning Department, trying to find out what she’s supposed to do. “They said I need a certificate of historical appropriateness, which means I have to file for a building permit,” she said. “It has to go through the building department, and the planning department has to review it and decide whether (the windows) are appropriate.”

According to City Planning Department spokesperson Gina Simi, the problem was that the repair required Polzine to replace the cracked framing around the window, not just the window pane. “The issue is not the design of the storefront system, but that the work itself needs to be legalized through the required city permit and entitlement process,” Simi wrote in an email. Because the building is a “designated historic resource,” any building permit Polzine obtains will require a historic review.

According to emails Polzine shared with The Chronicle, the city has given her until April 16 to file the paperwork and denied her request for an extension. At the moment, she has no idea how long the permit application process might take, nor its cost.

“It’s upsetting because it just doesn’t make sense,” Polzine said.