Arduino-SerialCommand | Arduino library to tokenize and parse commands

so following problem: I am currently writing a small program for my NUCLEO F207ZG which provides an interface for other services over the serial port. The goal of my program is to expose data with commands like ?variable and set values with !variable (eg. ?threshold returns 1400 and !threshold 1234 sets threshold to 1234). Additonally the variables in my program are synced with the EEPROM to persist the data.

For this whole process I've been given a codebase which includes a SerialCommands.h library.

The main problem is that setting values takes up way too much time and breaks the serial buffer (or something similiar) if other commands are executed immediatly after setting. I've written a few unit tests in python (using pyserial) that execute get requests (such as ?threshold) flawlessy, as often as possible. However, If I execute a set command (such as !threshold 1400) I need to wait AT LEAST four seconds before making any other requests, otherwise the serial interface/buffer seems to lose some data. The same thing happens if I try to make any set -> get requests on the Arduino Serial Monitor. Here is a short example:

1. ?threshold => returns '1400'
2. !threshold 1234
3. ?threshold => nothing happens
4. ?threshold => nothing happens
5. ?threshold => returns 'unrecognized command ???threshold' (see my code for this functionality)

EDIT: Something important which I forgot to mention. After the program has recovered (after step 5) the value can be queried correctly.

1. ?threshold => returns '1234'

I also have a blinking status LED (in 500ms steps) and if I set something the blinking stops noticeably for around a second.

So here is (non-working) simplified example of my codebase: