Advice needed on Building the Create and Alter Scripts step during App only upgrade from FSCM 8.9 to

We are upgrading from FSCM 8.9 to 9.1. This is an application upgrade only, tools version will remain the same. While running the Building the Create and Alter Scripts - Task 5-7-10, we are having below doubts.

1) We have some of the customized tables and fields. Now peoplesoft is trying to modify the customized fields and tables, so that it comes to its vanilla one. If this happpens there is a chance of data loss ( for fields whose length got reduced). How can we overcome this situation?
2) Lets say there is a table called JRNL_LN and delivered peoplesoft has 44 columns in version 8.9. Now peoplesoft has added one more column in version 9.1. But we have customized this table and added 40 more columns having total of 84 columns in our existing peoplesoft version 8.9. Now as peoplesoft added one more column in 9.1, there should be a total of 85 columns. Now in the alter script all the 85 columns are appearing but app designer definition contains 45 columns. Then how the alter script is picking all those customized columns. Peoplesoft is doing the