It's a little unclear exactly what you're doing, but I'm guessing it's something like this (code oversimplified but I hope it's clear):

sub myRunmodeA
{
my $self = shift;
my $isOK = blah (foo, bar)
...
}

sub myRunmodeB
{
my $self = shift;
fixBlahProblem();
...
}

sub blah
{
return if param('problem') eq 'true';
}
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What you want to do is, if myRunmodeA finds a problem, switch to myRunmodeB. There's nothing particularly magic about the run mode -- once your CGI::Application has been brought to life by the user, you are a class, so you can just call myRunmodeB, i.e. (using code from my example above):

sub myRunmodeA
{
my $self = shift;
if( blah (foo, bar) )
    {
    #usual code
    }
else
    { return $self->myRunmodeB; }
}
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(You might want to set the runmode before hopping into myRunmodeB, just for good luck. You probably do that with $self->{rm} = 'myRunmodeB', but this depends on how you set things up in CGI::Application:setup).

Hope that helps!

Alan