Please keep in mind that if you used Permalink Manager to save custom permalinks that are different from the original ones, they will not be used anymore after the plugin is removed from your site. This is due to the fact that Permalink Manager overwrites the WordPress core's permalink detecting functionality.
The inbuilt permalink system depends on rewrite rules, which are based on "regular expressions" that determine what content type should be loaded when a URL fits one of a set of permalink patterns. Contrary to this, Permalink Manager keeps all custom permalinks in an array so that they may be identified one by one, rather than using the patterns defined with original rewrite rules.