To quote the help for Read File:
"If byte stream type is wired and you need to read data created by LabVIEW 4.x or earlier, right-click this function and select Convert 4.x Data from the shortcut menu. In Convert 4.x Data mode, this function interprets the data in LabVIEW 4.x data storage layout and displays the icon for this function with a red 4.x on it. LabVIEW 4.x and earlier stores Boolean data in two bytes unless the data is in an array, in which case LabVIEW stores each Boolean element in a single bit. LabVIEW 5.0 and later stores Boolean values in a single byte, regardless of whether it is in an array. National Instruments recommends reworking any application that uses the Convert 4.x Data mode as a long term solution."
So, the change in binary file storage actually occured from LabVIEW 4.1 to 5.0. It would seem that you used the 4.1 format in your old 5.1 application. How many files do you have in the old format? A mass conversion should be possible. Get a list of all files (sorted by date or by folder), read them with the 4.1 conversion and write them back without the conversion. You might also be able to have a read VI that can handle both data types. Can you read a record with 4.1 format and do a test to see if it's valid? If it's not, through it away and read it again with the existing LabVIEW format.