Power Query Excel Refresh Done but data not getting updated

So if I understand correctly, you have 3 source queries for 3 folders and a consolidated query which appends all the 3 queries together and applies calculation, 

I would check the 3 source queries first. Filter out a row that you know is new and see whether you can see that row. If you cannot see the new row, then your data source address is wrong. 

If you can see the new row, then remove the filter and go on to the consolidated query. Add the same filter on the consolidated query right after the append step and see whether you can see the new rows. If you can see the new rows, then it maybe that one of the calculations is filtering out the new rows. If not, then you may not be appending the right queries.