we have some thoughts about general system performance, because we are having issues with system stability and also with data disappearing inside server after it successfully loaded from target.

problems begin usually if more than 15 targets are online same time and pushing to server a lot of different data. Problems increase when more targets are online same time.

1st - system hdd partitions distribution. we have seen that /usr partition is almost full most of times. generally /usr partition is meant to keep program files but your system is using this also caching incoming data and processing that data. if there are lot of data then this 9GB /usr partition size is clearly too small. also if system have issues you are always asking debug log what is also stored in /usr partition - one day debug log is up to 4GB and to store it to partition which have usually less than 3GB free space not very doable.
our suggestion - move caching data, logs, etc out of /usr partition or increase drastically /usr partition size up to at least 50-60GB, or even up to 100GB. in /boot partition for example have a lot of unused space 656GB total and using only 20MB. please think about re dimension hdd usage.

2nd - programs able to use all processor cores - we have seen that some of your program is not able to use full possibility of 8 cores what server is offer. ffmpeg2theora just for example is able to use only one core and if its working it takes 100 of one core. since ffmepg2theora is one of most important supporting program what is processing data inside server is clearly to visible that its one of system bottleneck.
our suggestion - implement or start using supporting programs what is able to use full power of system and not cause bottlenecks to data flow.

3rd - system linux distribution age and issues with old packets. Because you are not implemented to system any backup solution we set it up itself using ssh. In system have old ssh v5.3 what is just does not work well, it left sometimes some zombie ssh processes to running and after some tests we have observed that this probably causing server buffer overflow issue what we already reported several times.
our suggestion - start using newer debian release with allowing to keep up to date some essential programs like ssh