Hello, my name is Daniel León, I am a civil engineer with specialization in Geographic Information Systems using software such as ArcGIS Pro, ArcGIS Online, Dashboard, Story maps, ArcGIS hub, ArcGIS Experience Builder and Qgis.
In the first place the best thing to do would be to go to Google Earth Engine that allows us to process satellite images without so many restrictions and also we could achieve a temporal analysis of the images. With this software, which is free, we can obtain the images without so many colour mismatches.
Regarding the data limitations is because the acquisition of your images, or temporal resolution, is 16 days. Therefore, you will have a new satellite image updated for the same working area approximately every two weeks.
For your flood forecasting analysis with imagery we could determine the footprints of past floods in a time series that you can use to predict future floods but you will also need rainfall data. If you are interested in learning more about this, write to me and we can talk.
I invite you to send me a message to exchange more details of this proposal and discuss the best solutions you need.
Best regards
Daniel Leon