While I probably wouldn't use substr for this, I don't really see the number of (before or after) digits as being a problem. Here's a (multi-line) one-liner to explain:

$ perl -Mstrict -Mwarnings -E '
    my $find = q{#define MYVERSION };
    my $flen = length $find;
    my @strings = (
        q{#define MYVERSION 11},
        q{#define MYVERSION 9},
        q{#define MYVERSION 99}
    );
    for (@strings) {
        say;
        substr($_, $flen) = substr($_, $flen) + 1;
        say;
    }
'
#define MYVERSION 11
#define MYVERSION 12
#define MYVERSION 9
#define MYVERSION 10
#define MYVERSION 99
#define MYVERSION 100
[download]

Anyway, that's all fairly academic: I'm pretty sure I would have reached for something like s/^($find)(\d+)/$1.($2+1)/e in the first instance.

"we cannot be sure whether the version number has one or two or several digits"

Totally agree with you on that point.

Regards