Home plate apertures are designed to reduce or eliminate solder balls that occur when placing a chip and reflow of the solder. This aperture type is usually desired when processing with a "no-clean" solder paste. The design of the aperture is usually with a 30-50% reduction of paste below the chip end. Insufficient solder may occur. Look at the end caps of the chips, if there is at least 50% of the chip height soldered, then the aperture is probably not a cause of the failures.
Many other factors can come in to play to create the "gone south" syndrome. It could be coincidental with the stencil change. What paste is being used? Is the reflow profile validated for the components on board? How are the placements? Is there any ionic contamination? Are there a high fail rate of specific components? Have the PCB fab.'s been checked?
What about trying a limited run with the old stencils to see if the yield comes back up?
I could brain storm all day - what other details can you provide?
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