EXPORT saves the index informatino as well as the data information for the VSAM KSDS -- this is why you don't have to use DEFINE before an IMPORT. Changing an existing record won't impact the index information (unless, of course, you change the record length in which all bets are off). However, adding (or deleting) a record will change the index information and hence render the exproted file unusable as the index cannot be used any longer to rebuild the KSDS file.
If you want to modify (by adding to or deleling records from) the "backup" (and I use that word very cautiously since if you making changes to the output file and not the KSDS file, then you no longer have a "backup" file at all) then you MUST use REPRO to build a sequential file and then use DELETE / DEFINE to build the KSDS definnition anew before loading the data back again. Unless, of course, you spend the time to figure out the hexadecimal values that you must change to incorporate the changed index information in the exported file -- and don't forget that VSAM compresses the index keys so the process requires you to ALSO know how to rebuild compressed keys. And depending upon the specific changes, you might have to add a new level of index to the exported file, and so forth.
In other words, attempting to change an exported file the way you are doing is an EXTREMELY BAD idea for many, many, many reasons.