With today’s update to version 1.6, it is important to note that runs from previous versions will become incompatible. This is due to the extensive upgrades we have made to tracking run history in general.
If you have a run in progress in version 1.5 (or earlier), you will be prompted the following when you log in:

From here, you may either drop your current run entirely and begin anew in 1.6, or choose to downgrade your version and continue.
To downgrade your version on Steam, you must do the following:
Once you downgrade, however, you will need to re-update in order to start a new run.
When you begin your next run, you will be presented with this prompt:

In order to update to the latest version on Steam, you must do the following:

We apologize for the awkwardness of this process, but it was important to us to not disregard everyone’s current run in this update without any choice. Again, this is only due to the focus of this update being on improving run history information and providing more data for the player to collect. We do not plan for every update to be so inconvenient in this way.
Don't forget, you can always just choose to abandon your old run and skip all of the required version switching. We leave the decision up to you.
Thank you, and as always feel free to ask us questions here, or on our official Discord at discord.gg/Roguebook.