Hi Laurent,

I am running into same issue.

I have 1 solution to solve the problem, and the maximum file size to upload can be a bit over 4M.

Heap size limited for synchronous function is 6M while it is 12M for asynchronous fuction.

Any function inside   action.setCallback(this, function(a) { } is running asynchronously

so my solution is to call 

uploadChunk (cmp, file, fileName, fileContents, fromPos, toPos, attachId) 

inside action.setCallback(this, function(a) { }, and then make server side function as an asynchronous function

 @future
 public static void appendToFile(Id fileId, String base64Data)

To make it to be called in action.setCallback(this, function(a) { }

I created a method in controller(maybe there is a better way to setup and envoke action.setCallback) 

@AuraEnabled 
 public static void dummy(){ }

Then the uploadChunk method is something like below:

uploadChunk: function(cmp, file, fileName, fileContents, fromPos, toPos, attachId) {
        alert('uploadTest');
        // call this dummy fuction just for setting up action.setCallback
        var action = cmp.get("c.dummy"); 
        action.setCallback(this, function(a) {
            var action = cmp.get("c.saveFile"); 
            var chunk = fileContents.substring(fromPos, toPos);
    
            action.setParams({
                parentId: cmp.get("v.OrgInfo.Id"),
                fileName: fileName, // customised name
                base64Data: encodeURIComponent(chunk), 
                fileDescription: file.name,
                contentType: file.type,
                fileId: attachId
            });
       
            var self = this;
            action.setCallback(this, function(a) {
                var state = a.getState();
                if(state == "SUCCESS"){
                    attachId = a.getReturnValue();
                    fromPos = toPos;
                    toPos = Math.min(fileContents.length, fromPos + self.CHUNK_SIZE); 
                    // recrusive method 
                    if(fromPos < toPos) {
                        self.uploadChunk(cmp, file, fileName, fileContents, fromPos, toPos, attachId); 
                    }else{
                       alert('finishing');
                    }
                }
                if(state == "ERROR"){
                     alert('Error to upload document');
                }
            });         
            $A.enqueueAction(action); 
        });               
        $A.enqueueAction(action);   
    }

Also I believe using chunk instead of encodeURIComponent(chunk)

then in controller remove base64Data = EncodingUtil.urlDecode(base64Data, 'UTF-8'); can also increase a bit upload file size.

encodeURIComponent probably adds more characters into the content...

Hope this helps.

Cheers,
Ji