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As a temporary workaround I added the following to my import function: From the ids returned by the load() method, I search for corresponding ir_model_data entries, and update their 'noupdate' field to True.

res = partner_pool.load(cr, uid, field_names, partners, context=context)

if res['ids']:
    imd_pool = self.pool.get('ir.model.data')
    imd_ids  = imd_pool.search(cr, uid, [('res_id','in',res['ids']),('model','=','res.partner')], context=context)
    _logger.debug("Fixing external ids with no update = True on : %s" % imd_ids)
    if imd_ids:
        imd_pool.write(cr, uid, imd_ids, {'noupdate':True}, context=context)
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