It depends on the type of target "file" that you're uploading to.
If you're uploading to a member that has fixed block size (e.g., FB80), you'll need to ensure all the lines are padded out with spaces before you transmit it up (in binary mode).
Text mode transfers are not suitable for binary files (and your files are binary if they contain packed decimals - there's no reliable way for FTP to detect real line-end characters).
You'll need to fix your Windows ASCII-to-EBCDIC converter to be able to generate fixed length records.
The only other option is with a REXX script on the mainframe but this would still require being able to tell the difference between a real end-of-line marker and that marker within the binary data.
You could possibly tell the presence of a packed decimal by virtue of the fact that it consisted of BCD nybbles, the last of which is 0xC or 0xD, but that could also cause false positives or negatives.
My advice: when you convert it from ASCII to EBCDIC, pad out the lines to the desired record length at the same time.
The other point I'd like to raise is that if you just want to look at the files on the mainframe (not use them from any code that requires EBCDIC), the ISPF editor includes a few new commands (as of z/OS 1.9 if I remember correctly).
SOURCE ASCII
will display the data as ASCII rather than EBCDIC. In addition, the LF
command allows you to massage the ASCII stream in an FB member to correctly fix up line endings.