Unfortunately, this is a known issue (SNAP-662).
You can fix this by removing the valid-pixel expression from the bands, if you don’t need it.
or you can update the expressions.
In your case, you need to replace ‘c2rcc_flags_S3.Valid_PE_S3’ by ‘c2rcc_flags_S3.Valid_PE’
And for the other flags accordingly.
You can change the valid expression as follows:
nodes = result.getRasterDataNodes()
for n in nodes
validPixelExpression = n.getValidPixelExpression()
# Change expression
n.setValidPixelExpression(validPixelExpression)
Sorry, for the inconvenience this is causing. I hope it can be fixed soon.