The halachos of doing melacha are the same for Erev Shabbos and Erev Yom Tov since the point behind this prohibition is both to give appropriate time to prepare for Shabbos and Yom tov as well as to honor Shabbos and Yom tov.
The letter of the law is to stop from the time of Mincha Ketana any melachos that involve
- “Shihui” (concentration and ongoing involvement) and,
- Tircha (physical toil)
There is a discussion regarding exactly how to calculate the time of Mincha Ketana for this matter. (See Kaf Hachaim OC Siman 251:5 and also Shmiras Shabbos Kehilchasa ch42 note 118). Depending on how you calculate the time of Mincha Ketana for this matter it could fall out mid afternoon or it could fall out just a little before the time of candle lighting.
Prakmatia, which is mutar even after the time of Mincha Ketana (as per the Magen Avraham and the Mishneh Brurah in OC Siman 251), is defined as business dealings like buying and selling (Masah Umatan). It doesn’t seem from your question that this dispensation applies to your employees.
The poskim give examples of light tasks that are permissible even after the time of Mincha Ketana because they don’t involve Shihui or Tircha like writing letters, basic computer work, sewing a button, ironing, watering plants, simple household maintenance. These types of melachos are permissible after the time of Mincha Ketana even if you are getting paid, as is indicated clearly in the MB 252:2. However, in Shmiras Shabbos Kehilchasa ch42 note 133 he establishes that if any of these lighter activities are your Esek Kavuah (meaning your daily job) then they have the status of “Melachah” (meaning we treat them as if they involve Shihui and Tircha) and should be stopped at Mincha Ketana unless the person doing them literally needs the money they will earn to buy food to eat for that Shabbos.
There have also been Jews throughout the generations who were strict on themselves regarding this whole matter and stopped doing any Melacha either from the time of Mincha Gedolah, from mid-day, or even from when they had toiveiled for Shabbos even if it was before mid-day.
In summary, after considering all of the above, it seems that since the computer work is the “daily job” for your employees they have a legitimate claim to stop from the time of Mincha Ketana. As for exactly when that is, my sense is the custom in Klal Israel among Jews is to assume the earlier time of Mincha Ketana for this matter. So I don’t think you can expect them to work past that time on Erev Shabbos or Erev Yom Tov. If a particular employee claims to have a family custom to stop working from mid-day I think you should accommodate them.