Have noticed that the following 'hack' on the offending build.xml file will allow a 'Reload configuration from disk' operation to parse and load the missing build in the UI. Simply replace the offending <dfosFile> element with an empty <cachedContent> element.
So in the original example above:
replace
<dfosFile>/tmp/upload_6e074d3b_136c03af218__8000_00000013.tmp</dfosFile>
with
<cachedContent></cachedContent>

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