Just an update I have had no issue with the history generation today as the loop has now processed through 20 meta point recalculations with no issue creating complete sets of about 100000 values.
This metapoint logs every 5 minutes and it's the instant value, NaN isn't the culprit here..
ONLY when I check the delete beforehand or set that delete_first parameter to true does the issue of the zero's occur so it must be related to this somehow. Btw this checkbox is no big deal for me as I used the deletePointValuesBetween to purge all the point ranges.