Whne applying filters more rows are deleted that required. Not enough space for accur

I've written some code to take a lot of information from one format and turn it into something more useable. When i run the code with a sheet populated with 35000 lines or less it works fine and i get the desired results. It basically applies filters and deletes unwanted info. If i add more that 35000 lines after the filters are applied it deletes all rows rather than just those left visable by the filters.
Here is most of the code (too long to post all) which executes fine with 35000 lines or less

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This is the particular filter application and delete comand that is causing the problem. In the previous few lines it applies filters and deletes only the visible results. The lines of code are exactly the same except for these ones delete all lines rather than just the visible ones.

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Any help would be greatly appreciated

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