I’ll try and point you in right direction but it’s not a well trodden path I’m afraid. In fact since you are using emoncms.org I can not think of any way it can be done other than delete and replace.

For info see the Deleting old data and How to limit data size threads, but these apply to self hosted emoncms instances that you can access the raw data file on.

How many feeds are we talking of? and how many inputs do you have?
Can you post a screenshot of your inputs page so I can see the number of inputs and the complexity of the processing from the coloured tags?