There are 2 different types of caching in CA MDM.
1. Compression cache (C:\Program Files (x86)\CAMDM\data\Cache)
2. Differencing cache. (C:\Program Files (x86)\CAMDM\data\DiffCache)
Please do not delete them manually, as XCache.FAT and XDiffCache.FAT are permanent files and they store all the indexing information that is critical for Caching algorithm performance.
There is an easy way to Empty these folders by using "Empty" button on their respective pages
If there are cache files that are stale, then its better to check the following button. Remove files from differencing cache if the source file was not found during a differencing refresh
This will ensure only valid and relevant files are being cached, and stale files are being deleted whenever the relevant schedule runs (By default this is midnight of every day.). We would suggest to keep this button selected all the time as whe dealing with too many files.
The side effect of emptying these cache folders would be higher time in sending the files, resulting in higher session times, hence please do not do this during peak load.
The other approach to delete these cache files would be to click on "Show" button and understand which cache file belongs to what and delete it manually.