Is deactivating modules safe regarding settings? I had a strange error after uploading a module to a shared hosting server when going to admin/modules before even activating the module (image_desaturate_formatter).


  PDOException: SQLSTATE[23000]: Integrity constraint violation: 1062 Duplicate entry 'sites/all/modules/image_desaturate_formatter/image_desaturate_fo' for key 'PRIMARY': INSERT INTO {system} (filename, name, type, owner, info) VALUES (:db_insert_placeholder_0, :db_insert_placeholder_1, :db_insert_placeholder_2, :db_insert_placeholder_3, :db_insert_placeholder_4); Array ( [:db_insert_placeholder_0] => sites/all/modules/image_desaturate_formatter/image_desaturate_formatter.module [:db_insert_placeholder_1] => image_desaturate_formatter [:db_insert_placeholder_2] => module [:db_insert_placeholder_3] => [:db_insert_placeholder_4] => a:11:{s:4:"name";s:26:"Image Desaturate Formatter";s:4:"core";s:3:"7.x";s:7:"package";s:5:"Field";s:7:"project";s:26:"image_desaturate_formatter";s:12:"dependencies";a:2:{i:0;s:5:"field";i:1;s:5:"image";}s:7:"version";s:11:"7.x-2.0-rc1";s:9:"datestamp";s:10:"1356346648";s:11:"description";s:0:"";s:3:"php";s:5:"5.2.4";s:5:"files";a:0:{}s:9:"bootstrap";i:0;} ) in system_update_files_database() (line 2307 of xxx/htdocs/site/modules/system/system.module).


Now the update module isn't working anymore but just showing the following message, when I try to start the update process manually:


  Failed to get available update data for 27 projects.



Could the module upload error be related to the update module not working?
Is it safe to stepwise deactivate the modules to check if update isn't working due memory issues? Do I loose all the settings I've made?


EDIT/UPDATE:

I have limited access to server logs and there is a 


  The timeout specified has expired: ap_content_length_filter: apr_bucket_read() failed


and the "reports" section doesn't show anything except the PDO above.

I now have disabled every module except core and tried to run update in between with no effort. The update module isn't working anymore. Is there something else i could do?
It's impossible to say from here. Theoretically yes.
It depends on the module - a specific module could easily clear its variables in hook_disable(), or hook_uninstall(), or not at all. You'll have to check the install file for each module you disable to see how it will affect what you're doing. 


It sounds very much like you have two copies of the image_desaturate_formatter module in your Drupal install though; that could account for the error.

Regarding server logs - your host should give you access to these (I've never come across a host that would deny you access to your own logs, it's criminal!) so give them a call, they might have valuable information in them.