Berwind Industries of Junction City, KS received a contract to overhaul and repaint a number of Santa Fe boxcars. From the following references, I found some answers to your question: "Santa Fe Freight in Color...The Series Vol. 1-Boxcars" by Stephen Priest & Thomas Chenoweth published by Paired Rail Publications and "Santa Fe Box Cars-The Shock Control Era 1954-1995" by Charles Slater, published by the Santa Fe Railway Historical and Modeling Society Inc. The switch to Helvetica Gothic lettering as seen on the "J" cars-or 621553 and 621372 was adopted in March 1981. The Indian Red paint was replaced with mineral brown in 1986 when a decision was made to simplify the ATSF paint scheme. The two cars you illustrated were built by Pacific Car and Foundry in 1974 , Class Bx-166, Nos. 621300-621599, AAR designation XLI for general service. After looking at hundreds of photos of Santa Fe boxcars in these two books, the only similarly lettered car using what Atlas calls the "C" font was ATSF 622783, a class Bx-198, built by PC&F in 1979. These were single door XLIs, Nos. 622550-622783. The so-called "C" font strongly resembles the Conrail font and as Berwind is a contract operation, maybe they were doing work for Conrail and somebody used the wrong stencil on the Santa Fe cars, or the ATSF stencil got damaged and they used whatever was handy.
When Atlas announces a Santa Fe freight car that says Berwind Repaint in J or C.
I noticed a difference. Just the reporting marks using a different font.
Did year did the Santa Fe repainted their freight cars in J and C font?
Here in this picture is the J repaint.
http://www.rrpicturearchives.net/showPicture.aspx?id=1677264
Another one with the Holland Loading Snugger sign.
http://www.rrpicturearchives.net/showPicture.aspx?id=1470127
And the C repaint.
http://www.rrpicturearchives.net/showPicture.aspx?id=2009437
Amtrak America, 1971-Present.