if object_id('tempdb..#customers') is not null DROP TABLE #customers
GO
if object_id('tempdb..#temporary_storage') is not null DROP TABLE #temporary_storage
GO

SELECT [customer_number]
  INTO #customers 
  FROM [source_placeholder]

SELECT DISTINCT([customer_number]) AS 'customer_number'
  INTO #temporary_storage 
  FROM #customers 

    IF object_id('tempdb..#customers') is not null DROP TABLE #customers

GO --- End Batch here

SELECT * 
 INTO #customers
 FROM #temporary_storage

You can't put them in one batch, you have to put a GO between the drop statements.

Please do not get fooled by the error message.

Note that the error is table is full. It does not say disk is full.

What would create a table is full condition ?

It has to do with the changes that are pouring into the rollback segments for a transaction.

I have addressed this many times

• May 31, 2013 : How to solve "The table ... is full" with "innodb_file_per_table"?
• Mar 31, 2014 : mysql directory grow to 246G after one query, which failed due to table is full
• Jun 16, 2014 : MySQL Index creation failing on table is full
• Apr 07, 2015 : MySQL query INSERT INTO ... failed - The Table "x" is full

It appears that one of the following occurred

• The SELECT was in the middle of a transaction
• The SELECT attempted to hold too much rollback info in the face of many transactions

In either case, the tblinvoice table probably had so many changes pending that the SELECT just had to give up. This could have caused all write transactions against tblinvoice to rollback.

If you were running this SELECT on a busy Master with lots of writes against tblinvoice, then I could this SELECT having this problem.

What you should do is set up a reporting slave (running MySQL Replication) and run this type of query on it instead on the main server.

UPDATE 2018-02-27 10:10 EDT

Your problem may be the amount of RAM free.

You currently have this

tmp_table_size=2G
max_heap_table_size=2G

Try running the query again so that the temp table goes immediately to disk

set tmp_table_size = 1024 * 1024 * 16;
set max_heap_table_size = 1024 * 1024 * 16;
SELECT
    InvoiceNo,
    NetAmountAbs,
    InvoiceDate
  FROM tblinvoice
  WHERE GrossAmountAbs >= 200
  GROUP BY InvoiceNo,
           NetAmountAbs,
           InvoiceDate
  HAVING COUNT(*) > 1
  AND SUM(CASE WHEN NetAmount_Doc >= 0 THEN 1 ELSE 0 END) > 1
  AND MIN(AccountNumber) != MAX(AccountNumber)
  AND MAX(GrossAmountAbs) != MIN(GrossAmountAbs)
  AND MAX(ImportID) = 2;

Keep watch on the C:\Windows\SERVIC~2\NETWOR~1\AppData\Local folder. Watch the temp file that shows up in that folder. What I am hoping is that the temp table will reach the needed size on disk. Why ?

With tmp_table_size=2G and max_heap_table_size=2G, the temp table has to reach 2G in RAM before transferring to disk. My working theory is that you do not have 2GB of RAM free (We are talking Windows, right ???). This is why I am suggesting lowering these to 16M (which is the default value anyway). Give it a try !!!