Sometimes the fish go up through the locks at The Dalles, or so I've been told. Some fish have been known to go back down the ladders and thus be counted twice or more. I assume you're talking about end of season counts, as the daily numbers from some sites are occasionally missing.
The Deschutes also acts are a holding area for Idaho bound fish; fish go up as far as Pelton Dam and then turn around to continue on to Dworshak or wherever. But, as you point out, there should be attrition at every dam, as fish as siphoned off into the tributaries or are killed by nets, anglers, other predators, or disease. The season totals for fish passage should be greater at The Dalles than at John Day.
Someone else will probably provide the real explanation for this, but the locks may be a factor.
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