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having 2 classes with the same name, but a different memory layout in your program is a design desaster. (and the reason for your mysterious segfaults). use interfaces, virtual functions and inheritance instead:

// header:

struct MyProcessing {
       virtual ~MyProcessing() {}

       virtual bool func1(const Mat &input, Mat &output) = 0;
       virtual bool func2(Mat &input) = 0; // modify in-place
private:
       MyProcessing() {} // not allowed to use
};

// "factory" function
Ptr<MyProcessing> createMyProcessing();

// implementation:

struct MyProcessingImpl : public MyProcessing {
       bool func1(const Mat &input, Mat &output)  {
             ...
       }
       bool func2(Mat &input) {
             ...
       }

       Mat privateData;
       int foo;
};

// "factory" function, returns implementation class
Ptr<MyProcessing> createMyProcessing() { return makePtr<MyProcessingImpl>(); }

// usage

 Ptr<MyProcessing> process = createMyProcessing();
 Mat input = ...
 Mat output;
 process->func1(input, output);
 // no cleanup nessecary

// public (API) header:

struct MyProcessing {
       virtual ~MyProcessing() {}

       virtual bool func1(const Mat &input, Mat &output) = 0;
       virtual bool func2(Mat &input) = 0; // modify in-place
private:
       MyProcessing() {} // not allowed to use
};

// "factory" function
Ptr<MyProcessing> createMyProcessing();

// private implementation:

struct MyProcessingImpl : public MyProcessing {
       bool func1(const Mat &input, Mat &output)  {
             ...
       }
       bool func2(Mat &input) {
             ...
       }

       Mat privateData;
       int foo;
};

// "factory" function, returns implementation class
Ptr<MyProcessing> createMyProcessing() { return makePtr<MyProcessingImpl>(); }

// usage

 Ptr<MyProcessing> process = createMyProcessing();
 Mat input = ...
 Mat output;
 process->func1(input, output);
 // no cleanup nessecary