Approximately 60 jobs were lost earlier this month when the Czech company took the decision to migrate manufacturing from the site, which now serves as a support facility for the group's Czech operations.
The move marks a chequered 18 months since the company, which was founded by the late former Motherwell FC captain Matt Thomson, was acquired by the Czech multimedia business for an undisclosed sum.
In February this year, the company cut 55 jobs at the East Kilbride facility and last month, announced plans to shift production from the area as it "had not been immune to the current downturn in print manufacturing".
Unite had been in a dialogue with the owners, exploring "every avenue" possible.
Norman King, regional officer at Unite, said the owners had a number of choices with regards to the Thomson Litho site "and they took the last one".
"The manufacturing operations have now moved from there and it's a sad day for all concerned," he added.
According to the owners, the process was "vital" in determining the longer-term sustainability of the company and its viability of positioning the business as a "support function" to its parent company GZ Digital Media. GZ fulfils a broad portfolio of contracts across the UK and mainland Europe.
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