Use the following api to delete unwanted/unusable value set values
fnd_flex_values_pkg.delete_row (<<flex_Value_id
Flex value id can be select using the following select statement:
Select a.flex_value_id
From FND_FLEX_VALUES_VL a
,fnd_flex_value_sets b
Where a.FLEX_VALUE_SET_ID = b.FLEX_VALUE_SET_ID
And b.FLEX_VALUE_SET_NAME = 'XXPM_VALUE_SETNAME'
Don't use this for deleting application seeded value set values. Above solution can only be used for custom value sets.