You must have "noclobber" set, check the following example:
$ echo 1 > 1 # create file
$ cat 1
1
$ echo 2 > 1 # overwrite file
$ cat 1
2
$ set -o noclobber
$ echo 3 > 1 # file is now protected from accidental overwrite
bash: 1: cannot overwrite existing file
$ cat 1
2
$ echo 3 >| 1 # temporary allow overwrite
$ cat 1
3
$ echo 4 > 1
bash: 1: cannot overwrite existing file
$ cat 1
3
$ set +o noclobber
$ echo 4 > 1
$ cat 1
4
"noclobber" is only for overwrite, you can still append though:
$ echo 4 > 1
bash: 1: cannot overwrite existing file
$ echo 4 >> 1
To check if you have that flag set you can type echo $- and see if you have C flag set (or set -o |grep clobber).
Q: How can I avoid writing a blank file when my base command fails?
Any requirements? You could just simply store the output in a variable and then check if it is empty. Check the following example (note that the way you check the variable needs fine adjusting to your needs, in the example I didn't quote it or use anything like ${cmd_output+x} which checks if variable is set, to avoid writing a file containing whitespaces only.
$ cmd_output=$(echo)
$ test $cmd_output && echo yes || echo no
no
$ cmd_output=$(echo -e '\n\n\n')
$ test $cmd_output && echo yes || echo no
no
$ cmd_output=$(echo -e ' ')
$ test $cmd_output && echo yes || echo no
no
$ cmd_output=$(echo -e 'something')
$ test $cmd_output && echo yes || echo no
yes
$ cmd_output=$(myAPICommand.exe parameters)
$ test $cmd_output && echo "$cmd_output" > myFile.txt
Example without using a single variable holding the whole output:
log() { while read data; do echo "$data" >> myFile.txt; done; }
myAPICommand.exe parameters |log