To test, I would reload the QVD generated by QVWFILE1 back into QVWFILE1 to make sure it isn't an issue with the QVD export/import step. Right after the step in QVW FILE 1 where you STORE to QVD, DROP the table and then reload from QVD:
FROM pl source;
STORE PL_TABLE INTO [PL_TABLE.QVD] (qvd);
//After writing the table to QVD, drop it from the data model and replace it with QVD loaded version
DROP TABLE [PL_TABLE];
NOCONCATENATE LOAD * FROM [PL_TABLE.QVD] (qvd);
//Don't reuse original table name, keep the rename steps, because dropping and re-adding the same table name often
//causes suffix like [PL_TABLE-1]
RENAME TABLE QVD_PL_TABLE TO PL_TABLE;
Let the rest of the script finish, your final data model should be exactly the same. If the numbers in the P&L report do not change after you finish reloading QVWFILE1 while incorporating the QVD, then it looks like QVWFILE1 and the QVD export are not the problem. The problem lies with QVWFILE2 and may mean the chart attributes do not mirror the way they are assigned in QVWFILE1 or there are variable definitions that have changed.
If however upon completion of reload of QVWFILE1 that now reads from the QVD, you find that your P&L numbers have changed, then it may be an issue with data type reinterpretation upon reload from QVD. (i.e. check that the metadata tags for the calculation fields between QVWFILE1 and QVWFILE2 are not changing).