If you are deleting records from the 'part_ent_xref' table then it is the 'part_ent_xref' object that should be the subject of the DELETE task. This means that the $where clause which is passed to the DELETE task will contain the primary key of each selected entry in the format:
field1='value1' AND field2='value2'
If there are multiple selections each primary key will be enclosed in parentheses and separated by ' OR ', as in:
(field1='v1' AND field2='v2') OR (...) OR (...)
I have similar tables (PERSON and PERS_OPT_XREF) in the XAMPLE prototype which is included in the Radicore download, and I do not have an problem in deleting selected entries.
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