HELP! Patching zones causes all to disappear

[Realspace]

Sorry guys I need help. The patching process that seemed ok, I've done thousands of hand's replaces/add etc is eventually giving me serious problems.
The debug file shows no errors at start but later in-game is a mess.

I use patch method for all vanilla map but did not remove it entirely, I patched every entry o blocks. But seems the engine totally discards vanilla zones and only recognizes my added zones.

My zones.xml is made of ADD of new zones, so no replacement. But to eliminate inactive gates I made single removes like this:

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    <remove sel="//macro[@name='Zone005_Cluster_34_Sector001_macro']/connections/connection[@name='connection_ClusterGate034To009']">
</remove> 

I also tried not removing but replacing them, with am empty connection, to see if that could keep the zone untouched. But not.

To be sure they don't interfer I also moved all the replaces/removes at the beginning, then put the ADDS after and also tried adding the missing vanilla zones again. I did not remove any in sector.xml. Fact is they disappear, the entire zones not only the connections I targeted. I noticed this after seeing god.xml missing a lot of stations. So patched every entry in god.xml to target a different zone, but the problem remains that zones are no more there and I can't know for what they could be needed. I used this method for the aim of letting vanilla zones as much possible untouched, otherwise I could more easily replace the entire file.

This thing is causing a ton of problems with vanilla god and other things that seem not to find the zone in the map, but the zone was not removed by me only the connection containing a gate ref.

Is the debug-log reliable in-game?

I get these msgs:

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[=ERROR=] 0.00 No matching node for path '//macro[@name='Zone005_Cluster_34_Sector001_macro']/connections/connection[@name='connection_ClusterGate034To009']' in patch file 'extensions\xrsge\maps\xu_ep2_universe\zones'. Skipping node.

Like that the node I removed was already missing, which is silly because it is a gate in vanilla game. If I don't add these removes I'll have a lot of inactive gates allaround

and the god engine

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[=ERROR=] 0.00 [GodEngine] God Entry ID: 'frf_defence_cluster_411_sector001' could not find zone 'zone001_cluster_411_sector001_macro'.

..and this is scary:

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[=ERROR=] 0.00 [GodEngine] God Entry ID: 'Story_ScrapyardStation' could not find zone 'zone006_cluster_502_sector001_macro'.

because I don't even touch that zone in my mod, only add other zones...where has it gone??

[Realspace]

I am figuring out something. Seems to me that the patching procedure is not that fluid. When patching a lot of things and expecially patching the dlc's.

I noticed that god missed expecially dlc's stations even if I had not been changing any. I really tried every possible combinatiom. This happens even using vanilla "gods", something from the dlc's is missing.

So I also removed all the maps from the dlc's and added to the patched vanilla map, this already accomplishes something. Then created a new God file with all dlc's gods all added in one, as total replacement and boom, it works well, not missing any station.

It seems to me that everything that is not in the main directory of the mod but in its extensions is not read well by the engine that misses some node. Patching a patch, so to say, is not viable.

Finally, to patch the dlcs seems to me that you have to first remove the content you want to modify and then duplicate it in the mod''s main assets.

EDIT: This worked indeed. I removed all the maps vanilla+dlcs and removed also all god files. Then I added new ones filled with original+new content. Now everything works perfectly, god does not miss a single station and debuglog has no errors. Hope this information is useful to others