You should always load to a struct. That makes it clear where variables come from. Then it is also easier to extend the struct instead of creating a new struct every time like you're doing.
% --- Executes on button press in saveBeats.
function saveBeats_Callback(hObject, eventdata, handles)
% hObject handle to saveBeats (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
if exist('beatData.mat','file')
S=load('beatData.mat');beatData=S.beatData;
else
beatData = struct('filename',{},'numberOfBeats',{}); %creation of simple struct with two fields: 'filename' and 'numberOfBeats')
end
currentFileName = getappdata(0,'currFile'); %gets the name of current audiosample
currentBeats = get(handles.numBeats,'Value'); %gets the number of beats written in the edit box
currentIndex = get(handles.listbox1,'Value'); %gets the index of the current audiosample from a listbox
beatData(currentIndex).filename = currentFileName; %saves the name of the audiofile to 'filename'-field in the struct beatData at index
beatData(currentIndex).numberOfBeats = currentBeats; %saves the number of beats
save('beatData.mat', 'beatData'); %save the struct as a .mat file
