If the SACD ISO is ripped from an SACD, I suspect that something else is wrong. I have hundreds of SACD ISOs and thousands of SACDs and this isn't a common problem.
I don't believe SACD ISOs use cue sheets, per se. The last time I examined one, they contain a UDF file system, and that contains the tracks as DFF or DSF or such files, one per track, and sometimes DST (lossless) compressed. So the only way to manipulate the "cue sheet" would be to append the raw DSD data of all the files together, then re-split it into new DFF/DSF files. They will also need to be re-compressed into DST format, if they were compressed to start with.