I lyophilized a sample which still had a water content and I have returned to undergo a second lyophilization process. I want to ensure that the water is extracted. Could this spoil the sample lyophilization excess?
it depends on the nature of your sample. Protein might go through denaturation with an excessive lyophilization process especially the concentrated protein solution, otherwise I don't think samples will be spoiled.
The protocol depends on the type of material. In our case, we did a lyophilization protocol bearing in mind the knownledge of the sample (transition temperature, ...). I don't know how a plant sample will behave. Sorry.