Here are improved answers with awk and sed.
Unlike the other answers, these work independent of what the 'Filename:' path is. That is to say, if you change './debs/' to './myDebs/' it will still work. All they require is that '.deb' file is at the end of the path
Sed
sed '/Filename:/s|^\(.*/\)\([^\.]*\)\..*$|\1download.php?p=\2|' ./infile
awk
awk -F'/' '/Filename:/{split($NF,a,".");$NF="download.php?p=" a[1]}1' OFS='/' ./infile
Input
$ cat ./infile
Package: com.xyz.abc
Version: 1.0
Filename: ./debs/abc.deb
Package: com.xyz.def
Version: 1.0.0-1
Filename: ./MyDebs/def.deb
sed Output
$ sed '/Filename:/s|^\(.*/\)\([^\.]*\)\..*$|\1download.php?p=\2|' ./infile
Package: com.xyz.abc
Version: 1.0
Filename: ./debs/download.php?p=abc
Package: com.xyz.def
Version: 1.0.0-1
Filename: ./MyDebs/download.php?p=def
awk Output
$ awk -F'/' '/Filename:/{split($NF,a,".");$NF="download.php?p=" a[1]}1' OFS='/' ./infile
Package: com.xyz.abc
Version: 1.0
Filename: ./debs/download.php?p=abc
Package: com.xyz.def
Version: 1.0.0-1
Filename: ./MyDebs/download.php?p=def