You could start with trying to figure out the detail level entries.
Get the individual timesheet sums from prtimeentry.pract sum.
That will relate to the timeperiods where the entries are.
If your actuals are back to 2013 they are not to be in the daily slices.
prassignment does not daily actuals either.
What you can do to get the daily actuals is to use OWB with a tabulated view for actuals.
First compare the weekly actuals to the actuals from the timesheets per timeperiod (assuming you have weekly timeperiods)
If you see a a difference change the view to daily to get the daily values.
Then you can create a custom timeslice for timeentries for that timeperiod only to get the daily entries. If you want you can also create a custom slice for the daily actuals for that period.
The custom slices will contain limited amount of data so the effect in performance should not be paralyzing and afterwards you can delete the custom slices.
That will allow you to see if there is a timeentry not reflected in the actuals.
Then look at the individual WIP entries to see if all you see in the daily actuals are there.
If there is an error in one or more entries or an entry is missing create WIP adjustments as needed.