Hiya Phoenix,
These are questions you need to ask the CC team itself rather than the user to user help on the forums.
The only thing I would have any possible thoughts of are if you are waiting a long time between updates (in other words, not updating for a lot of updates and then updating a very old version to a very new version that has been revamped extremely since your last update). This would cause issues at times as many times a lot of programs get full rewrites in certain parts of the program or things are just changed quite a bit since your last update and the settings themselves are changed.
Anyways, if you've kept up to date all along, then you shouldn't be losing your information. I update Direct FTP pretty much every time it's updated and pretty much right away, same for most of the programs I use from CC which is a good handful. I have only had this issue if they updated something quite extremely, or if there's an issue which usually needs to be reported to the CC Team.
I would definitely open a support topic with the CC support system and ask them about it.