This plugin was originally intended for use with Lord of the Rings mod (1.7.10) servers, where terrain generation algorithms change regularly and players want to use the latest mod version, which leads to frequent map resets and a hassle to backup/restore all places containing players builds... (the LOTR mod is not mandatory).

What is currently available in the 1.00 version:

a serie of marking commands to select regions, chunks and areas for later backup. The resulting lists are stored in per player text files. They are saved/reloaded at player's logout/login.
a serie of marking commands for reporting issues (generation, griefing, offensive builds, corruption) to the server admin. The resulting list is stored in a text file along with the UIDs of the reporting players. It is saved/reloaded at server stop/start.
a command to reset map (dimension) using all the players maps for instructions on what to keep.
- as a side note, this command can selectively delete chunks in a region file.
a command to verify the integrity of 1 or all region files in a dimension.

What is coming next:

console commands to prune or merge region files.
console commands to raise/lower the height of individual regions & chunks.
console commands to smooth generation issues at regions/chunks borders.
console commands to import massive builds in a server from pruned region files, resolving local variation of blocks & items IDs on the fly and automatically smoothing the builds borders with the existing terrain.

Full explanations are available on the plugin web site (wiki tab) and the source code is available on GitHub (source tab).

Minecraft Region Manager