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The stability of fluorescently labeled oligos and fluorophore function is similar to the stability of a standard oligo.
IDT recommends oligos that are to be stored long term should be stored frozen, at –20°C. If the oligos are going to be resuspended, storage in a TE buffer such as IDTE (10 mM Tris, 0.1 mM EDTA, pH 7.5–8.0) is better than using water (non-DEPC treated). The impact from the type of storage medium used is marginal at –20°C, but becomes more important at higher temperatures (see the DECODED™ article, Storing oligos: 7 things you should know, for the data).
With fluorophores, it’s important to remember that exposure to natural light or ozone can negatively impact stability. If fluorescently modified oligos will be exposed to sustained light, protective cover from the lighting source (e.g., using brown tubes and/or foil covering) should be considered.
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