{
    "components": {
        "comp1": {
            "base": {
                "app": {
                    "ioIn": {
                        "in24v": [2242, 2245],
                        "ntc": [2941, 2940],
                        "flow1": [10356185, 10356197]
                    }
                }
            }
        },
        "comp2": {
            "base": {
                "app": {
                    "ioIn": {
                        "in12v": [1234, 1237],
                        "ntc": [7, 8],
                        "flow2": [9, 10]
                    }
                }
            }
        }
    }
}

$json = json_decode($jsonStr); // load as json object

iterate($json, $myData, $path);

function iterate($json, &$data = array(), &$path = '')
{
	if(is_object($json))
	{
		foreach($json as $k => $v)
		{
		
			if(is_array($json->$k)) // last level with values [old, new]
			{
				$data[$path.$k] = $json->$k[1]; // store as associative array
				continue;
			}
			
			$path .= $k.'.';
			iterate($json->$k, $data, $path);
			$path = ''; // reset path				
		}		
	}
	else
	{
		// do nothing
	}
}

{
    "components": {
        "comp1": {
            "base": {
                "app": {
                    "ioIn": {
                        "in24v": 2245,
                        "ntc": 2940,
                        "flow1": 10356197
                    }
                }
            }
        },
        "comp2": {
            "base": {
                "app": {
                    "ioIn": {
                        "in12v": 1237,
                        "ntc": 8,
                        "flow2": 10
                    }
                }
            }
        }
    }
}

function getNewValueWithPath(&$data, $path = '', &$result = []) {
    foreach ($data as $key => &$value) {
        $newPath = $path ? "$path.$key" : $key;
        if (is_object($value)) {
            getNewValueWithPath($value, $newPath, $result);
        } else {
            $result[$newPath] = $value[1];
        }
    }
}

$data = json_decode($json, false);
getNewValueWithPath($data,'',$result);

$output = json_encode($result, JSON_PRETTY_PRINT);
echo $output;

{
    "components.comp1.base.app.ioIn.in24v": 2245,
    "components.comp1.base.app.ioIn.ntc": 2940,
    "components.comp1.base.app.ioIn.flow1": 10356197,
    "components.comp2.base.app.ioIn.in12v": 1237,
    "components.comp2.base.app.ioIn.ntc": 8,
    "components.comp2.base.app.ioIn.flow2": 10
}

			$path .= $k.'.';
			iterate($json->$k, $data, $path);
			$path = ''; // reset path				

			iterate($json->$k, $data, $path.$k.'.');