However, the OP clearly states:
Saves from previous versions to 0.98 are not supported.
They are
not supported meaning that using them on newer releases will cause the game either to
crash or at least to pop up a non-blocking
exception (gray screen that can be skipped by clicking on "Ignore").
But I've been told by another player that even using saves from v0.98 or superior on a newer release
- even if not triggering any formal error message - can cause the quest log to malfunction, so he suggested me to restart from scratch.
Since minor releases are monthly or so, I restarted from scratch only when v0.98 came out.
My quest log was "clear" at the end of content just once (probably that one time in which I played from start to end v0.98 using only saves made with v0.98).
All the other times, some hint remained in the quest log even after completion.
E.g. Talk to Fred even when I found the clients for him and the only option clicking on him is "I'll come later".
The same goes with "keep practicing with Falsetto" or "meet Barbara at work", etc, after those arcs are completed so no more action is possible.
I just cheated on money, weather, hunger, and things like that, and never on relevant stats like courage, rethoric, etc.