Using a custom template that after moving servers is causing blocks to duplicate.

[OPTIOUS]

Upon moving hosting servers, we have encountered this issue where making any kind of change to the modules featured on the template, that will cause the changes to duplicate even if it's only a simple change. The last time this happened it was merely the database duplicating the value and was able to fix it by doing edits directly into the database. However this time there is nothing wrong with the database value. Looked for alternatives but have come up short. Need to know if there is a possible fix for this issue to prevent it from happening or should I push them to update/change their template. 

Thanks in advance.