Can through-hole leads be cut filed level with the PCB back while maintaining good connectivity?

I'm looking at using a through hole mounted CR2016 battery holder on a circuit but the leads need to be level with the back of the PCB due to size constraints. 

You can, but cutting leads flush after soldering stresses the joint significantly. Cutting them prior to soldering means you may not be able to get a good solder joint, requiring either re-soldering or 10x visual inspection.

Since the battery and holder have significant mass, the strength of the joints is important so you might want to do some testing (such as drop testing).

This is not standard handling, so it will be up to the PCBA house whether they want to do it and how much they want to charge.

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Oliver Smith

Oliver is an experienced electronics engineer skilled in PCB design, analog circuits, embedded systems, and prototyping. His deep knowledge spans schematic capture, firmware coding, simulation, layout, testing, and troubleshooting. Oliver excels at taking projects from concept to mass production using his electrical design talents and mechanical aptitude.
Picture of Oliver Smith

Oliver Smith

Oliver is an experienced electronics engineer skilled in PCB design, analog circuits, embedded systems, and prototyping. His deep knowledge spans schematic capture, firmware coding, simulation, layout, testing, and troubleshooting. Oliver excels at taking projects from concept to mass production using his electrical design talents and mechanical aptitude.

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