After I fixed permissions and synced some files they got deleted from my Dropbox folder

I don't think you're running into issues with file names. Dropbox handles file names with periods in them just fine. The only exception to that is when you're on windows and the period is at the end (either after the extension, or perhaps if there is no extension like on a folder name). Those names are illegal on windows, and so we don't currently download them to windows devices. (tangentially, we're currently rolling out a feature to allow these files to sync down: https://help.dropbox.com/sync/flexible-filenames)

I believe what went wrong here is roughly:
* We keep a list of files that are running into permission errors, so we don't spin CPU re-checking those all the time
* If there are any changes on the server that need to be downloaded, where the corresponding file on the local machine is running into a permission error, we mark that as "unreconstructable" for similar reasons - essentially "pretending" that the file doesn't exist, again so we don't waste CPU. (this only applies to the local state - so the file on the server, supposing it existed, would be fine)
* Anyway - when you fixed the permission error, I think what happened is that we didn't remove that file from the list of files known to be spinning on permission errors quickly enough, and it ended up getting marked (incorrectly!) in this "unreconstructable" state (if it wasn't already in that state, which it might have been)
* "unreconstructable" is a state we only keep in memory as the sync engine is running, so restarting the client naturally clears this state and we keep running.
* What should happen is should be detecting that we're no longer getting permissions issues, and we should unset all those related states in the engine, so you don't have to restart the client.

This is certainly unintended, and I've filed a bug internally so we fix this up.