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I had a similar issue when I initially installed Klipper on my Ender 3 S1 (not the plus). It would not connect unless I fully restarted Octoprint whenever I turned on the printer. The change I needed to make was go into settings in Octoprint (though I assume its similar on other front ends), and add the following settings:
Serial Port: /tmp/printer
Baud Rate: 11520
If that is not the case for you, try to add some more details. Do you have the config file correct?
I'll look for baudrate, but doesn't explain why it's work when I flash the firmware again...
Can you provide any more details on what is not working and what might have changed since things stopped working? There is not a lot of info to go on.
I've been running Klipper on a Raspberry pi with an Ender 3 S1 Pro for about 8 months with virtually zero hiccups, but I'd hardly claim to be an expert.
It work for me since the last year but start buggin this week.
The bltouch les stay red (might turn purple when the boot is done)