SOS-Config ruined after dist-up. Back to previous version old LinuxCNC dist?

To my horror today as i returned to check my configuration i realised that something goes terribly wrong. First as i open AXIS 4 errors pop up:

STEPGEN: Channel 1: The requested maximum velocity of 1252 step/sec is too high
STEPGEN: The maximum possible frequency is 1250 steps/second

and the same 2 for channel 2.
Secondly i jogged the five joints. Two of them work just fine. However the other 3 are messed up. Specifically, both + and - buttons used for jogging, move the joint to the same direction.

From what I'm told the only thing that changed since yesterday that all were fine is that this morning they "apt-get update" and "apt-get dist-upgrade". The dist-upgrade did the 3 availables upgrades to linuxcnc, linuxcnc-doc and a third (which they didn't remember). But can a dist change so drammatically that reads the same information as the previous one but interpets them differently?

From what i see the configuration files are intact(hal, ini, etc), but the result is catastrophe. Is there a way to roll back to the version i was? Can anything be done to check what changed?

Linux X004 3.4-9-rtai-686-pae #1 SMP PREEMPT Debian 3.4.55-4linuxcnc i686 GNU/Linux

Now its the 2.9.0-pre0-653-gb25997c. The previous i'm not sure The previous official branch is v2.9.0-pre0-645-g0742250 right? ( source ) So that's probably it? Actually i haven't had and upgrade for a week so im not quite sure

For the past 4 months definitely master because I wanted the Joint-Axes changes. Before that I had 2.7.14. However the change has been done several months now and the configuration was stable

The update happened through terminal with dist-upgrade. Can it be undone with synaptic manger then? Even to a little older stable version, for example two weeks ago?

Yes it's the same config. Actually the only config I have set on that pc. I start LinuxCNC and pick the config. Nothing special actually. That's why I'm so panicked. It seems very strange to me too.