You think your solution works because your script to create the test file and your script to dump the test file suffers from the same bug as your solution. Your demonstration only shows that you can convert CRCRLF to CRLF.

The first f.txt contains foo\r\r\nbar\r\r\nstuff.

>perl -e "print \"foo\r\nbar\r\nstuff\";" > f.txt

>debug f.txt
-rcx
CX 0011
:
-d100 l11
0AF7:0100  66 6F 6F 0D 0D 0A 62 61-72 0D 0D 0A 73 74 75 66   foo...bar
+...stuf
0AF7:0110  66                                                f
-q
[download]

You alter it to foo\r\nbar\r\nstuff.

>perl -i.bak -pe "s/\r(?=\n)//" f.txt

>debug f.txt
-rcx
CX 000F
:
-d100 lf
0AF7:0100  66 6F 6F 0D 0A 62 61 72-0D 0A 73 74 75 66 66      foo..bar.
+.stuff
-q
[download]

why doesn't it work??

Unless you use binmode on your input file, CRLF gets converted to LF on read.
Unless you use binmode on your output file, LF gets converted to CRLF on write.