On the light tube, that will work fine for the plants. It is a bit "warmer" white [the lower the kelvin rating, the warmer, the higher the kelvin the cooler] than I prefer, but that is a visual issue to us. The plants will use the red and blue fine. Java Fern
should not be nburied in the substrate, at least not the rhizome (the thick "root" bit) or it will likely rot; it should be attached to wood or rock, either gently wdedging the rhizome in a crevice, or using some black cotton thread or fishing line. After a few weeeks the hair roots will attach the plant.
On the substrate, in a 25g tank I would change the entire substrate at one go rather than in stages. Yes, some nitrifying bacteria will be lost, but there is also bacteria on all surfaces covered by water, including plant leaves, wood, rock, tank walls, filter tubes, etc. The easiest way I have found to do this is to drain some tank water (from the top so it is relatively "clean") into a spare tank or even a bucket, move the plants and any pieces of wood or rock into this and then the fish, and then drain the main tank and remove the substrate. Do not clean or rinse the filter. Add the new substrate, replace wood and rock (if any), fill the tank with fresh tap water, condition it as soon as it starts to fill (to avoid killing off bacteria), recommenct the filter and heater, return the plants, and lastly the fish. Net them from the temporary tank back into the main tank; no need to use the dirty water.